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  • Climate change  (19)
  • Bacteria  (13)
  • Frontiers Media  (18)
  • American Institute of Physics (AIP)
  • Lagos (Nigeria)
  • Milano: Fondazione Eni Enrico Mattei (FEEM)
  • Nature Publishing Group
  • 1
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Stunz, E., Fetcher, N., Lavretsky, P., Mohl, J., Tang, J., & Moody, M. Landscape genomics provides evidence of ecotypic adaptation and a barrier to gene flow at treeline for the arctic foundation species Eriophorum vaginatum. Frontiers in Plant Science, 13, (2022): 860439, https://doi.org/10.3389/fpls.2022.860439.
    Description: Global climate change has resulted in geographic range shifts of flora and fauna at a global scale. Extreme environments, like the Arctic, are seeing some of the most pronounced changes. This region covers 14% of the Earth’s land area, and while many arctic species are widespread, understanding ecotypic variation at the genomic level will be important for elucidating how range shifts will affect ecological processes. Tussock cottongrass (Eriophorum vaginatum L.) is a foundation species of the moist acidic tundra, whose potential decline due to competition from shrubs may affect ecosystem stability in the Arctic. We used double-digest Restriction Site-Associated DNA sequencing to identify genomic variation in 273 individuals of E. vaginatum from 17 sites along a latitudinal gradient in north central Alaska. These sites have been part of 30 + years of ecological research and are inclusive of a region that was part of the Beringian refugium. The data analyses included genomic population structure, demographic models, and genotype by environment association. Genome-wide SNP investigation revealed environmentally associated variation and population structure across the sampled range of E. vaginatum, including a genetic break between populations north and south of treeline. This structure is likely the result of subrefugial isolation, contemporary isolation by resistance, and adaptation. Forty-five candidate loci were identified with genotype-environment association (GEA) analyses, with most identified genes related to abiotic stress. Our results support a hypothesis of limited gene flow based on spatial and environmental factors for E. vaginatum, which in combination with life history traits could limit range expansion of southern ecotypes northward as the tundra warms. This has implications for lower competitive attributes of northern plants of this foundation species likely resulting in changes in ecosystem productivity.
    Description: This research was made possible by funding provided by NSF/PLR-1417645 to MM. The Botanical Society of America Graduate Student Research Award and the Dodson Research Grant from the Graduate School of the University of Texas at El Paso provided assistance to ES. The grant 5U54MD007592 from the National Institute on Minority Health and Health Disparities (NIMHD), a component of the National Institutes of Health (NIH) provided bioinformatics resources and support of JM.
    Keywords: Arctic ; Climate change ; Eriophorum vaginatum ; Landscape genomics ; Environmental niche modeling ; Genotype-environment association analyses ; Refugia
    Repository Name: Woods Hole Open Access Server
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  • 2
    Publication Date: 2022-10-31
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in O’Brien, J., McParland, E. L., Bramucci, A. R., Ostrowski, M., Siboni, N., Ingleton, T., Brown, M. V., Levine, N. M., Laverock, B., Petrou, K., & Seymour, J. The microbiological drivers of temporally dynamic Dimethylsulfoniopropionate cycling processes in Australian coastal shelf waters. Frontiers in Microbiology, 13, (2022): 894026, https://doi.org/10.3389/fmicb.2022.894026.
    Description: The organic sulfur compounds dimethylsulfoniopropionate (DMSP) and dimethyl sulfoxide (DMSO) play major roles in the marine microbial food web and have substantial climatic importance as sources and sinks of dimethyl sulfide (DMS). Seasonal shifts in the abundance and diversity of the phytoplankton and bacteria that cycle DMSP are likely to impact marine DMS (O) (P) concentrations, but the dynamic nature of these microbial interactions is still poorly resolved. Here, we examined the relationships between microbial community dynamics with DMS (O) (P) concentrations during a 2-year oceanographic time series conducted on the east Australian coast. Heterogenous temporal patterns were apparent in chlorophyll a (chl a) and DMSP concentrations, but the relationship between these parameters varied over time, suggesting the phytoplankton and bacterial community composition were affecting the net DMSP concentrations through differential DMSP production and degradation. Significant increases in DMSP were regularly measured in spring blooms dominated by predicted high DMSP-producing lineages of phytoplankton (Heterocapsa, Prorocentrum, Alexandrium, and Micromonas), while spring blooms that were dominated by predicted low DMSP-producing phytoplankton (Thalassiosira) demonstrated negligible increases in DMSP concentrations. During elevated DMSP concentrations, a significant increase in the relative abundance of the key copiotrophic bacterial lineage Rhodobacterales was accompanied by a three-fold increase in the gene, encoding the first step of DMSP demethylation (dmdA). Significant temporal shifts in DMS concentrations were measured and were significantly correlated with both fractions (0.2–2 μm and 〉2 μm) of microbial DMSP lyase activity. Seasonal increases of the bacterial DMSP biosynthesis gene (dsyB) and the bacterial DMS oxidation gene (tmm) occurred during the spring-summer and coincided with peaks in DMSP and DMSO concentration, respectively. These findings, along with significant positive relationships between dsyB gene abundance and DMSP, and tmm gene abundance with DMSO, reinforce the significant role planktonic bacteria play in producing DMSP and DMSO in ocean surface waters. Our results highlight the highly dynamic nature and myriad of microbial interactions that govern sulfur cycling in coastal shelf waters and further underpin the importance of microbial ecology in mediating important marine biogeochemical processes.
    Description: This research was supported by the Australian Research Council Grants FT130100218 and DP180100838 awarded to JS and DP140101045 awarded to JS and KP, as well as an Australian Government Research Training Program Scholarship awarded to JO’B.
    Keywords: DMSP ; DMS ; DLA ; Phytoplankton ; Bacteria ; qPCR ; 16S rRNA gene ; 18S rRNA gene
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  • 3
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Winters, G., Teichberg, M., Reuter, H., Viana, I. G., & Willette, D. A. Editorial: seagrasses under times of change. Frontiers in Plant Science, 13, (2022): 870478, https://doi.org/10.3389/fpls.2022.870478.
    Description: Awareness of the ecological importance of seagrasses is growing due to recent attention to their role in carbon sequestration as a potential blue carbon sink (Fourqurean et al., 2012; Bedulli et al.), as well as their role in nutrient cycling (Romero et al., 2006), sediment stabilization (James et al., 2019), pathogen filtration (Lamb et al., 2017), and the formation of essential habitats for economically important marine species (Jackson et al., 2001; Jones et al.). Despite their importance and the increasing public and scientific awareness of seagrasses, simultaneous global (e.g., ocean warming, increase in frequency and severity of extreme events, introduction and spread of invasive species) and local (e.g., physical disturbances, eutrophication, and sedimentation) anthropogenic stressors continue to be the main causes behind the ongoing global decline of seagrass meadows (Orth et al., 2006; Waycott et al., 2009).
    Description: This research was partially funded through the BMBF project SEANARIOS (Seagrass scenarios under thermal and nutrient stress: FKZ 03F0826A) to HR and MT. MT was partially funded through the DFG project SEAMAC (Seagrass and macroalgal community dynamics and performance under environmental change; TE 1046/3-1). IV was supported by a postdoctoral research grant Juan de la Cierva-Incorporación (IJC2019-040554-I) and from MCIN/AEI /10.13039/501100011033 (Spain).
    Keywords: Seagrasses ; Climate change ; Eutrophication ; Responses of seagrasses to single and combined stressors ; Spatial-temporal modeling
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  • 4
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Smith, A. R., Mueller, R., Fisk, M. R., & Colwell, F. S. Ancient metabolisms of a thermophilic subseafloor bacterium. Frontiers in Microbiology, 12, (2021): 764631, https://doi.org/10.3389/fmicb.2021.764631.
    Description: The ancient origins of metabolism may be rooted deep in oceanic crust, and these early metabolisms may have persisted in the habitable thermal anoxic aquifer where conditions remain similar to those when they first appeared. The Wood–Ljungdahl pathway for acetogenesis is a key early biosynthetic pathway with the potential to influence ocean chemistry and productivity, but its contemporary role in oceanic crust is not well established. Here, we describe the genome of a novel acetogen from a thermal suboceanic aquifer olivine biofilm in the basaltic crust of the Juan de Fuca Ridge (JdFR) whose genome suggests it may utilize an ancient chemosynthetic lifestyle. This organism encodes the genes for the complete canonical Wood–Ljungdahl pathway, but is potentially unable to use sulfate and certain organic carbon sources such as lipids and carbohydrates to supplement its energy requirements, unlike other known acetogens. Instead, this organism may use peptides and amino acids for energy or as organic carbon sources. Additionally, genes involved in surface adhesion, the import of metallic cations found in Fe-bearing minerals, and use of molecular hydrogen, a product of serpentinization reactions between water and olivine, are prevalent within the genome. These adaptations are likely a reflection of local environmental micro-niches, where cells are adapted to life in biofilms using ancient chemosynthetic metabolisms dependent on H2 and iron minerals. Since this organism is phylogenetically distinct from a related acetogenic group of Clostridiales, we propose it as a new species, Candidatus Acetocimmeria pyornia.
    Description: Metagenome sequencing was made possible by the Deep Carbon Observatory Census of Deep Life supported by the Alfred P. Sloan Foundation and was performed at the Marine Biological Laboratory (Woods Hole, MA, United States). This work was funded by NASA grant NNX08AO22G and a graduate fellowship from the NSF Center for Dark Energy Biosphere Investigations. The flow cells were funded under J0972A from the U.S. Science Support Program of Joint Oceanographic Institutions.
    Keywords: Metabolism ; Carbon fixation ; Acetogenesis ; Bacteria ; Seafloor ; Hydrogen ; Amino acid ; Clostridia
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  • 5
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24208 | 19325 | 2018-05-19 06:39:34 | 24208 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: The microbial load of four different fish species from five different market locations in Ibadan metropolis were determined using standard microbiological procedures. The bacteria count of fish sampled from Ojo market was the highest while the bacteria count of the fish sample from Bodija market was the lowest. There was no significant difference (p〈0.05) in the microbial load of the fish sampled from various market locations in Ibadan metropolis. Similarly, there was no significant difference (p〉0.05) in the microbial load on various fish species sold in Ibadan metropolis. The isolated bacteria from the study were: E. coli, Salmonella spp, Klebsiella spp, Staphylococcus aureus, Aerosomonas spp, Pseudomonas spp, Vibrio spp, Serratia spp, Chromobacterium spp, Enterobacteria spp and Shigella spp. The fungi count of fish sampled from Omi markets was the highest while the fungi count of the fish sampled from Ojo market was the lowest. The following fungi were however isolated from the study: Aspergillus flavus, Penicillium spp, Fusarium oxysporum, Trrichoderma spp and Ceotrichium albidium. The study shows that reheating may be necessary to destroy or inactivate micro-organisms in smoked fish before consumption.
    Description: Includes: 2 tables and 2 figures.;Also includes: 17 refernces.
    Keywords: Fisheries ; Nigeria ; Ibadan ; Bacteria ; Fungi ; Market ; Fish species ; freshwater environment ; Microbial contamination ; Microorganisms ; Bacteria ; Freshwater fish ; Cured products ; Sample contamination ; Fungi ; Public health ; Quality assurance ; Disinfection
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24583 | 19325 | 2018-05-20 15:55:56 | 24583 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: This paper examines the major effects of climate charge on aquaculture, especially on the freshwater ecosytem. Aquaculture as established is not practiced evenly across the world. Therefore, the paper highlights the current aquaculture practices within the regions and across the different environments to ascertain the major effects of climate variations on the freshwater ecosystem and aquaculture practices in particular. The main elements of climate change that would impact on aquaculture produ ction, such as sea level and temperature rise, changes in monsoon patterns and extreme climatic events and water stress, among others were properly looked at and the reasons for their effects addressed. The different elements of climate change that are experienced in varying degrees can be either positive or negative or directly or indirectly, depending on the different culture systems that are practiced. It is in the process of our study that we brought out the complex attributes of climate change as it affects aquaculture productivity and the possible roles that the society can play to ameliorate the harsh effects of this ugly monstet; referred to as ”climate change and the consequent global warming trends.
    Description: Includes: 17 references.
    Keywords: Atmospheric Sciences ; Aquaculture ; Nigeria ; Climate change ; Freshwater ; Aquaculture ; freshwater environment ; automation
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  • 7
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24592 | 19325 | 2018-05-20 16:08:17 | 24592 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: The effect of climate change on the aquatic environment has been well documented with results detailing increase in green house gases and global temperature. Water quantity and quality for aquaculture is also affected by this global phenomenon. Increasing global temperatures affects many sectors in an ecosystem. Water use in aquaculture can be in-situ or ex-situ. Groundwater is expected to be recharged if climate change leads to increased rainfall and runoff but empirical evidence suggests otherwise. The sustainability of groundwater for aquaculture is therefore threatened. Increased temperatures of surface waters can affect water quality and suitability for use in aquaculture with attendant biofouling and growth of thermophilic algae. Rainwater is affected by human activities and pollution as well as materials used for its collection. It is usually low in pH and will need to be buffered. The use of water from any source as well as the use of water bodies for aquaculture must be done with regular analysis of parameters since climate change is an ongoing process.
    Description: 34 references.
    Keywords: Atmospheric Sciences ; Aquaculture ; Nigeria ; Groundwater ; Surface water ; Rain water ; Climate change ; Aquaculture ; automation
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  • 8
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24601 | 19325 | 2018-05-21 12:17:22 | 24601 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Climate change has the potential to severely impact coastal and inland environments and ecosystems, and by extension fisheries and aquaculture. Coastal regions of the world are already experiencing flooding due to rise in sea level. In recent times, salinization of coastal areas due to flooding from storm surges and high tidal influence has been observed. Aquaculture is a fast growing agri-business venture in Nigeria presently and many coastal communities derive their livelihood from it. The culture of freshwater fish species that are very sensitive to high salinity may be threatened leading to mortality of stocked fish and loss of livelihood for coastal population. Consequently, there is urgent need for development and domestication of the Silver catfish, Chrysichthys nigrodigitatus that can tolerate higher salinity more than Mudcatfish (Clarias gariepinus). This will help mitigate the impact of salinization of coastal areas arising from sea water flooding on culture of fresh water fish species.
    Description: Includes: 17 references.
    Keywords: Aquaculture ; Pollution ; Fisheries ; Chrysichthys nigrodigitatus ; Clarias gariepinus ; Nigeria ; Climate change ; Silver catfish ; Chrysichthys nigrodigitatus ; freshwater environment ; automation
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  • 9
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24667 | 19325 | 2018-05-27 15:06:16 | 24667 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: The study identified the perception of fish farmers in Oyo State to climate change as well as the adaptation strategies used by them. A two stage stratified sampling method was used to select 156 fish farmers from the four Agriculture Development Programme (ADP) zones and eight local government areas (LGAs) in Oyo State. Structured questionnaires were administered to the fish farmers. Descriptive statistic and linear regression were used to analyses data collected. The result shows that majority were males (84.0%\}, dominant age (66.0%) were within the age bracket of 46-65 years. The farmers are literate as 46.8% have attained secondary education, 69.9% had above six years of experience in fish farming experience and 97.5% were engaged in culturing catfish Clarias spp. The highest portion (70.5%) earns less than N500,000 as income from fish sale. Due to effect of climate change on fish production in the study area, fish farmers reported different types of adaptation strategies. Result of the linear regression analysis indicates that there is a significant (p〈0.05) negative effect of household size and years of fish farming experience and significant (p〈0.1) positive effect of age on farmers' perception of climate change on fish production.
    Description: Includes: 7 references.
    Keywords: Aquaculture ; Pollution ; Nigeria ; Agriculture development programme ; Climate change ; Fish farmers ; freshwater environment ; automation
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  • 10
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24584 | 19325 | 2018-05-20 15:57:28 | 24584 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Climate change will have significant impacts on Nigeria's freshwater and marine aquatic systems. and hence on the countries fisheries and aquaculture. Fisheries and aquaculture are highly vulnerable to changes in weather pattern. and the impacts, which could be negative or positive, will vary from the coastal areas to the drier northern parts of the country. Elevated water temperalures will affect fish physiological processes, thereby affecting spawning. survival of the juveniles, recruit into the exploitable phase of population, population size, production and yield. The impacts of increased flooding of the freswater bodies will be negative through erosion of watershed, destruction of fish feeding and breeding habitats, decrease in primary productivity and alteration of the normal resilience of the aquatic systems, or positive in expansion of aquatic habitats for primary and fish productions especially during the dry season. Drought will exacerbate draw down of the lakes and reservoirs, and insufficient flow in the river hasins for spawning and primary pro duction thereby affecting fish production. Rise in the water level of the Atlantic ocean will lead to intrusion of more salty wafer into The river delta areas, and inundation of the coastal low-lying areas, thus affecting distribution of both the freshwater and marine fishes as a result of changes in the physical and chemical properties of the waters. The impacts will ultimately affect fish population, production and supply, thereby affecting the livelihood of over 26 million people engaged in the primary and secondary sectors of the fisheries industry, as well as food security of the country. The adaptation and mitigation strategies will be based on the peculiar characteristics and interactions of fisheries and aquaculture within the framework of feasible policy instruments. Strategies and policy measures need to be evolved to combat the observable and projected impacts of climate change on fisheries and aquaculture, in order to protect the livelihoods of the fishing communities and food security.
    Description: Includes: 13 references.
    Keywords: Atmospheric Sciences ; Aquaculture ; Fisheries ; Nigeria ; Climate change ; Fisheries ; Aquaculture ; Impacts ; Mitigation ; Food security ; freshwater environment ; automation
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  • 11
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24629 | 19325 | 2018-05-22 06:30:19 | 24629 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: The estuarine catfish, Chrysichthys nigrodigitatus, is a prized food fish in Nigeria especially in the Niger Delta region. There is a growing concernrn over the sustainability of the fishery in the face of climate change and environmental variability. Studies were conducted on the fecundity, gonadosomatic index and the spawning period of the species. The objectives were to determine the average fecundity of the species and to use the gonadosomatic index to determine its spawning period with the aim of proffering management advice and prerequisites of the species in the face of climate change. A total of 44 females and 40 males were used for the study which spanned the period from May 2011 to April 2012. The fecundity of the species ranged from 3,730.5 eggs to 41,535.9 eggs. There was correlation between the total fecundity and fish weight (p~,01, r= 0.80, n= 44). The regression model for the relationship was expressed as fecundity = 4660.8+4.76 weight. The gonadosomatic index was highest in the month of May and dropped sharply in june signifying that spawning in Chrysichthys nigrodigitatus starts around this period. The implications of these findings in respect to sustainability of the species, and its aquaculture in the face of climate change are discussed.
    Description: Includes: 14 references.
    Keywords: Fisheries ; Atmospheric Sciences ; Chrysichythys nigrodigitatus ; Nigeria ; Lower Cross River ; C. nigrodigitatus ; Reproduction ; Climate change ; Cross Rivber ; Sustainability ; freshwater environment ; automation
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  • 12
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24661 | 19325 | 2018-05-27 14:57:38 | 24661 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: The study examined fisher folk responses to climate change in Kainji lake basin. The sample comprises of fisher folks within and New Bussa. Eighty questionnaires were administered to obtain the primary data and analysed using descriptive and inferential statistical tools. The results revealed that majority (70%) of the respondent were male, however (61.2%) of them had tertiary education. Majority (60%) of the respondents were aware of changes in climate in the area. Majority (65%) and (55%) of the respondents were involved in incidence of deforestation and charcoal production respectively. In conclusion, it was discovered that little knowledge about climate change and its effects were found among fisher folk. Therefore it recommends that sensitization workshops/lectures be done to enable the fisher folk have adequate knowledge on climate change and the implications on fisheries activities in the basin.
    Description: includes: 11 references.
    Keywords: Pollution ; Fisheries ; Nigeria ; Climate change ; Fisher folk ; Fishing community ; Awareness ; freshwater environment ; automation
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  • 13
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24166 | 19325 | 2018-05-13 18:40:22 | 24166 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Probiotics are a promising feed additive to stimulate animal growth and secure a low disease response in aquaculture industry where there are high stocking densities in shrimp and fish production. Fermented locust beans (Parkia biglobosa) are known to be rich in protein and used as food condiment. Probiotic bacteria were isolated from this locally available food material. Culture and characterizations of isolates were carried out. Sugar fermentation patterns were determined by using an API 50 CHL system and incubation were performed anaerobically at 37~'C. MRS broth culture grown at 37~'C overnight was added to 9ml of MRS Agar and the bacteria were incubated at 37~'C for 24 and 48 hrs. Discrete and single colony of lactobacillus was isolated using colony morphology and biochemical tests. The most significant viable taxa isolated was Lactobacillus fermentum at a pH range of (3.0-8.0), while the least viable taxa isolated was Leuconostoc mesenteroides ssp. Microscopically they were Grampositive, rod shaped, non- motile, catalase negative and absence of Endospore.
    Description: Includes: 2 tables and 2 plates.;Also includes: 15 references.
    Keywords: Aquaculture ; Nigeria ; Lagos ; Locust bean ; Probiotics ; Lactobacillus ; Probiotics ; freshwater environment ; Feed ; Additives ; Aquaculture ; Microorganisms ; Bacteria ; Disease resistance ; Fermented products ; Fish culture ; Shrimp culture
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24224 | 19325 | 2018-05-19 07:11:26 | 24224 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Jabi Lake is a natural water body in Abuja Federal Capital Territory (FCT). It was expanded for commercial fishing following relocation of Nigeria's headquarters to Abuja in 1993. Quantitative analysis of microbiological status of water and fish from the Lake was carried out. Samples were collected from the dam site, open water, middle lake and inlet. Result reveal that total coliform count which are indicators of pollution are high (2.0 x 103 cfu/ml, 1.1 x 103 cfu/ml, 1.0 x 103 cfu/ml and 1.1 x 103 cfu/ml for dam site, open water, middle lake, and inlet respectively). Total viable count too is high (9.2 x 103 cfu/ml, 4.9 x 103 cfu/ml, 4.6 x 103 cfu/ml and 4.9 x 103 cfu/ml for dam site, open water, middle lake and inlet respectively). There are no coliform bacteria in the muscle of the fish. High bacterial load is an indication of biological pollution and these calls for restraint on the side of those who are using the lake as site for refuse dump.
    Description: Includes: 10 references.
    Keywords: Fisheries ; Pollution ; Nigeria ; Jabi Lake ; Jabi lake ; Water ; Fish ; Bacteria ; freshwater environment ; Microbiology ; Fish ; Pollution ; Water pollution ; Lake fisheries ; Fishery surveys ; Bacteria ; Baseline studies ; Water sampling ; Microbial contamination ; Muscles ; Freshwater fish ; Pollution surveys ; Water analysis ; Freshwater pollution
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24185 | 19325 | 2018-05-16 14:41:02 | 24185 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Bacteria has been implicated in food poisoning, and smoked fish is not an exception.Generally, fish is highly susceptible to spoilage; therefore this study evaluated the bacteria load in smoked fish from three major locations in Shiroro area of Niger State namely; Gwada, Kuta and Zumba.The smoked fish samples collected from these locations were smeared at both the gills and head regions of the fishes. The bacteria samples identified were Escherichia coli, Bacillus subtilis, Staphylococcus aureus, Staphylococcus epidermis, Pseudomonas aeruginosa, and Samonella typhi, which were common to all the three locations sampled, while only Streptococcus feacaliswas only was found to be present in both Kuta and Zumba location.The frequency of occurrence of these 68 bacteria samples isolated ranges from 8 - 20%, with Bacillius subtilis having the highest occurrence and Pseudomonas aeruginosa have the least occurrence. Out of the total 68 samples, 14 skin samples (20.6%) and 5 gills samples (7.4%) exceeded the acceptable limits of total mesophilic aerobic counts which were 10〈sup〉6〈/sup〉 - 10〈sup〉7〈/sup〉 cfu/g. In the case of total coliform counts, 12 skin samples (17.6%) and 7 gills samples (10.3%) exceeded the acceptable limit which is 4.0 x 102, while in the case of Staphylococcus aureus, 4 skin samples (5.9%) and 2 gills samples (2.9%) exceeded the acceptable limit which is 103 cfu/g. Similarly 3 skin samples (4.4%) and 1 gill sample (1.5%) exceeded the acceptable limit of Salmonella typhi which is 104 cfu/g.
    Description: Includes: 4 tables.;Also includes: 21 references.
    Keywords: Fisheries ; Health ; Escherichia coli ; Bacillus subtilis ; Staphylococcus aureus ; Staphylococcus epidermis ; Pseeudomonas aeruginosa ; Nigeria ; Shiroro L. ; Bacteria ; Smoked (Clarias spp) fish ; Location and recommended values ; brackishwater environment ; freshwater environment ; marine environment ; Bacteria ; Food poisoning ; Cured products ; Fish ; Fish spoilage ; Acceptability ; Lake fisheries ; Gills ; Brain ; Evaluation
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24222 | 19325 | 2018-05-19 07:06:04 | 24222 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: A total of 2,800 tilapia (Oreochromis niloticus) were stocked in seven duplicates 5 by 4 m2 earthen ponds in NIFFR Integrated Farm, New-Bussa, Niger-State. Raw and sterilized poultry manure of 0.13 to 0.52 kg/m3 concentrations were used to fertilize the ponds with the unfertilized ponds serving as control. The following bacteria were isolated from the cow dung manure; Escherichia coli, E. co1iOl57:H7, Aeromonas hydrophila,Salmonella typhi, Shigella dysenteriae and Staphylococcus aureus. The fish samples from the 0.13 and 0.26 kg/m3 sterilized manure fertilized ponds had zero count in the muscles while samples from other ponds had pathogens in their fish muscles. The study revealed that fish samples from sterilized manures were better in terms of microbial safety for fish productions hence sterilized manure are recommended for use in fish production to ensure the microbial safety of the fish, handlers and that of the consumers.
    Description: includes: 13 references.
    Keywords: Aquaculture ; Oreochromis niloticus ; Escherichia coli ; Aeromonas hydrophila ; Samonela typhi ; Shigella dysenteriae ; Staphylococcus aureus ; Nigeria ; Niger State ; Catfish ; Pathogens ; Microbial quality ; Raw and sterilized manue ; freshwater environment ; Bacteria ; Freshwater fish ; Fish culture ; Fish ponds ; Manure ; Microorganisms ; Freshwater aquaculture ; Aquaculture products ; Food fish ; Quality assurance ; Muscles ; Microbial contamination
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  • 17
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    FISON | Lagos (Nigeria)
    In:  http://aquaticcommons.org/id/eprint/24596 | 19325 | 2018-05-20 16:13:09 | 24596 | Fisheries Society of Nigeria
    Publication Date: 2021-07-15
    Description: Sixty apparently healthy Heterobranchus bidorsalis and Clarias anguillaris from NIFFR were cultured and 30 each from Monai and wara villages as wild environments were obtained for the studies. The total bacterial load varied from 2.2 x l05 to 1.08 x l08 and 2.27 x 105 to 6.3 x l08 CFU/g of the skin of C. anguillaris and H.bidorsalis in the culture respectively, while the load varied from 1.77 x 105 to 1.17 x l08 and 2.27 x 105 to 9.0 x l07 CFU/g in the wild respectively. Eleven bacterial general species were identified which include: Bacillus species B.firmus, Pseudomonas species, P. aeruginosa, Escherichia coli, Klebsiella aerogenes, K. ozaenae, Staphylococcus aureus, Streptococcus species, S.faecalis, and Aeromonas species. The aims of this investigation is to compare the type and the load of bacteria isolates on the skin of catfish in both culture and wild environment.
    Description: Includes: 7 references.
    Keywords: Aquaculture ; Fisheries ; Clarias anguillaris ; Heterobranchus bidorsalis ; Nigeria ; Kainji L. ; Comparative study ; Bacteria ; Skin ; Clarias ; Heterobranchus ; Kainji Lake ; freshwater environment ; automation
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  • 18
    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bernhard, J. M., Wit, J. C., Starczak, V. R., Beaudoin, D. J., Phalen, W. G., & McCorkle, D. C. Impacts of multiple stressors on a benthic foraminiferal community: a long-term experiment assessing response to ocean acidification, hypoxia and warming. Frontiers in Marine Science, 8, (2021): 643339, https://doi.org/10.3389/fmars.2021.643339.
    Description: Ocean chemistry is changing as a result of human activities. Atmospheric carbon dioxide (CO2) concentrations are increasing, causing an increase in oceanic pCO2 that drives a decrease in oceanic pH, a process called ocean acidification (OA). Higher CO2 concentrations are also linked to rising global temperatures that can result in more stratified surface waters, reducing the exchange between surface and deep waters; this stronger stratification, along with nutrient pollution, contributes to an expansion of oxygen-depleted zones (so called hypoxia or deoxygenation). Determining the response of marine organisms to environmental changes is important for assessments of future ecosystem functioning. While many studies have assessed the impact of individual or paired stressors, fewer studies have assessed the combined impact of pCO2, O2, and temperature. A long-term experiment (∼10 months) with different treatments of these three stressors was conducted to determine their sole or combined impact on the abundance and survival of a benthic foraminiferal community collected from a continental-shelf site. Foraminifera are well suited to such study because of their small size, relatively rapid growth, varied mineralogies and physiologies. Inoculation materials were collected from a ∼77-m deep site south of Woods Hole, MA. Very fine sediments (〈53 μm) were used as inoculum, to allow the entire community to respond. Thirty-eight morphologically identified taxa grew during the experiment. Multivariate statistical analysis indicates that hypoxia was the major driving factor distinguishing the yields, while warming was secondary. Species responses were not consistent, with different species being most abundant in different treatments. Some taxa grew in all of the triple-stressor samples. Results from the experiment suggest that foraminiferal species’ responses will vary considerably, with some being negatively impacted by predicted environmental changes, while other taxa will tolerate, and perhaps even benefit, from deoxygenation, warming and OA.
    Description: This work was supported by the US NSF SEES-OA grant OCE-1219948 to JB and the Investment in Science Program at WHOI. DM also received support from the NSF Independent Research and Development Program.
    Keywords: Deoxygenation ; Ocean acidification ; Benthic communities ; Benthic foraminifera ; Climate change ; Propagule bank ; Global warming
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  • 19
    Publication Date: 2022-05-25
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Beam, J. P., Becraft, E. D., Brown, J. M., Schulz, F., Jarett, J. K., Bezuidt, O., Poulton, N. J., Clark, K., Dunfield, P. F., Ravin, N. V., Spear, J. R., Hedlund, B. P., Kormas, K. A., Sievert, S. M., Elshahed, M. S., Barton, H. A., Stott, M. B., Eisen, J. A., Moser, D. P., Onstott, T. C., Woyke, T., & Stepanauskas, R. Ancestral absence of electron transport chains in Patescibacteria and DPANN. Frontiers in Microbiology, 11, (2020): 1848, doi:10.3389/fmicb.2020.01848.
    Description: Recent discoveries suggest that the candidate superphyla Patescibacteria and DPANN constitute a large fraction of the phylogenetic diversity of Bacteria and Archaea. Their small genomes and limited coding potential have been hypothesized to be ancestral adaptations to obligate symbiotic lifestyles. To test this hypothesis, we performed cell–cell association, genomic, and phylogenetic analyses on 4,829 individual cells of Bacteria and Archaea from 46 globally distributed surface and subsurface field samples. This confirmed the ubiquity and abundance of Patescibacteria and DPANN in subsurface environments, the small size of their genomes and cells, and the divergence of their gene content from other Bacteria and Archaea. Our analyses suggest that most Patescibacteria and DPANN in the studied subsurface environments do not form specific physical associations with other microorganisms. These data also suggest that their unusual genomic features and prevalent auxotrophies may be a result of ancestral, minimal cellular energy transduction mechanisms that lack respiration, thus relying solely on fermentation for energy conservation.
    Description: This work was funded by the USA National Science Foundation grants 1441717, 1826734, and 1335810 (to RS); and 1460861 (REU site at Bigelow Laboratory for Ocean Sciences). RS was also supported by the Simons Foundation grant 510023. TW, FS, and JJ were funded by the U.S. Department of Energy Joint Genome Institute, a DOE Office of Science User Facility supported under Contract No. DE-AC02-05CH11231. NR group was funded by the Russian Science Foundation (grant 19-14-00245). SS was funded by USA National Science Foundation grants OCE-0452333 and OCE-1136727. BH was funded by NASA Exobiology grant 80NSSC17K0548.
    Keywords: Bacteria ; Archaea ; evolution ; genomics fermentation ; respiration ; oxidoreductases
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  • 20
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scalpone, C. R., Jarvis, J. C., Vasslides, J. M., Testa, J. M., & Ganju, N. K. Simulated estuary-wide response of seagrass (Zostera marina) to future scenarios of temperature and sea level. Frontiers in Marine Science, 7, (2020): 539946, doi:10.3389/fmars.2020.539946.
    Description: Seagrass communities are a vital component of estuarine ecosystems, but are threatened by projected sea level rise (SLR) and temperature increases with climate change. To understand these potential effects, we developed a spatially explicit model that represents seagrass (Zostera marina) habitat and estuary-wide productivity for Barnegat Bay-Little Egg Harbor (BB-LEH) in New Jersey, United States. Our modeling approach included an offline coupling of a numerical seagrass biomass model with the spatially variable environmental conditions from a hydrodynamic model to calculate above and belowground biomass at each grid cell of the hydrodynamic model domain. Once calibrated to represent present day seagrass habitat and estuary-wide annual productivity, we applied combinations of increasing air temperature and sea level following regionally specific climate change projections, enabling analysis of the individual and combined impacts of these variables on seagrass biomass and spatial coverage. Under the SLR scenarios, the current model domain boundaries were maintained, as the land surrounding BB-LEH is unlikely to shift significantly in the future. SLR caused habitat extent to decrease dramatically, pushing seagrass beds toward the coastline with increasing depth, with a 100% loss of habitat by the maximum SLR scenario. The dramatic loss of seagrass habitat under SLR was in part due to the assumption that surrounding land would not be inundated, as the model did not allow for habitat expansion outside the current boundaries of the bay. Temperature increases slightly elevated the rate of summer die-off and decreased habitat area only under the highest temperature increase scenarios. In combined scenarios, the effects of SLR far outweighed the effects of temperature increase. Sensitivity analysis of the model revealed the greatest sensitivity to changes in parameters affecting light limitation and seagrass mortality, but no sensitivity to changes in nutrient limitation constants. The high vulnerability of seagrass in the bay to SLR exceeded that demonstrated for other systems, highlighting the importance of site- and region-specific assessments of estuaries under climate change.
    Description: This research was supported by the National Science Foundation Research Experience for Undergraduates Program (OCE-1659463), the Woods Hole Oceanographic Institution Summer Student Fellowship Program, the Barnegat Bay Partnership (through a US EPA Clean Water Act grant to Ocean County College; CE98212313), and the USGS Coastal and Marine Hazards/Resources Program. Although this project has been funded in part by the United States Environmental Protection Agency pursuant to a grant agreement with Ocean County College, it has not gone through the Agency’s publications review process and may not necessarily reflect the views of the Agency; therefore, no official endorsement should be assumed. Any use of trade, firm, or product names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
    Keywords: Seagrass (Zostera) ; Climate change ; Spatial model ; Sea level rise ; Temperature ; North American Atlantic Coast ; Regional ; Eelgrass (Zostera marina)
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  • 21
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wagner, S., Schubotz, F., Kaiser, K., Hallmann, C., Waska, H., Rossel, P. E., Hansmann, R., Elvert, M., Middelburg, J. J., Engel, A., Blattmann, T. M., Catala, T. S., Lennartz, S. T., Gomez-Saez, G., V., Pantoja-Gutierrez, S., Bao, R., & Galy, V. Soothsaying DOM: A current perspective on the future of oceanic dissolved organic carbon. Frontiers in Marine Science, 7, (2020): 341, doi:10.3389/fmars.2020.00341.
    Description: The vast majority of freshly produced oceanic dissolved organic carbon (DOC) is derived from marine phytoplankton, then rapidly recycled by heterotrophic microbes. A small fraction of this DOC survives long enough to be routed to the interior ocean, which houses the largest and oldest DOC reservoir. DOC reactivity depends upon its intrinsic chemical composition and extrinsic environmental conditions. Therefore, recalcitrance is an emergent property of DOC that is analytically difficult to constrain. New isotopic techniques that track the flow of carbon through individual organic molecules show promise in unveiling specific biosynthetic or degradation pathways that control the metabolic turnover of DOC and its accumulation in the deep ocean. However, a multivariate approach is required to constrain current carbon fluxes so that we may better predict how the cycling of oceanic DOC will be altered with continued climate change. Ocean warming, acidification, and oxygen depletion may upset the balance between the primary production and heterotrophic reworking of DOC, thus modifying the amount and/or composition of recalcitrant DOC. Climate change and anthropogenic activities may enhance mobilization of terrestrial DOC and/or stimulate DOC production in coastal waters, but it is unclear how this would affect the flux of DOC to the open ocean. Here, we assess current knowledge on the oceanic DOC cycle and identify research gaps that must be addressed to successfully implement its use in global scale carbon models.
    Description: This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) project number 422798570. The Hanse-Wissenschaftskolleg and the Geochemical Society provided funding for the conference. Additional support was provided by the National Science Foundation OCE #1756812 to SW. TB acknowledges funding from ETH Zürich and JAMSTEC. JM was supported by the Netherlands Earth System Science Centre. SP-G was funded by COPAS Sur-Austral (CONICYT PIA APOYO CCTE AFB170006). GG-S acknowledges funding from DFG, DI 842/6-1.
    Keywords: Dissolved organic carbon ; Global carbon cycle ; Recalcitrance ; Isotopic probing ; Climate change
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  • 22
    Publication Date: 2022-10-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Benthuysen, J. A., Oliver, E. C. J., Chen, K., & Wernberg, T. Editorial: advances in understanding marine heatwaves and their impacts. Frontiers in Marine Science, 7, (2020): 147, doi:10.3389/fmars.2020.00147.
    Description: Editorial on the Research Topic Advances in Understanding Marine Heatwaves and Their Impacts In recent years, prolonged, extremely warm water events, known as marine heatwaves, have featured prominently around the globe with their disruptive consequences for marine ecosystems. Over the past decade, marine heatwaves have occurred from the open ocean to marginal seas and coastal regions, including the unprecedented 2011 Western Australia marine heatwave (Ningaloo Niño) in the eastern Indian Ocean (e.g., Pearce et al., 2011), the 2012 northwest Atlantic marine heatwave (Chen et al., 2014), the 2012 and 2015 Mediterranean Sea marine heatwaves (Darmaraki et al., 2019), the 2013/14 western South Atlantic (Rodrigues et al., 2019) and 2017 southwestern Atlantic marine heatwave (Manta et al., 2018), the persistent 2014–2016 “Blob” in the North Pacific (Bond et al., 2015; Di Lorenzo and Mantua, 2016), the 2015/16 marine heatwave spanning the southeastern tropical Indian Ocean to the Coral Sea (Benthuysen et al., 2018), and the Tasman Sea marine heatwaves in 2015/16 (Oliver et al., 2017) and 2017/18 (Salinger et al., 2019). These events have set new records for marine heatwave intensity, the temperature anomaly exceeding a climatology, and duration, the sustained period of extreme temperatures. We have witnessed the profound consequences of these thermal disturbances from acute changes to marine life to enduring impacts on species, populations, and communities (Smale et al., 2019). These marine heatwaves have spurred a diversity of research spanning the methodology of identifying and quantifying the events (e.g., Hobday et al., 2016) and their historical trends (Oliver et al., 2018), understanding their physical mechanisms and relationships with climate modes (e.g., Holbrook et al., 2019), climate projections (Frölicher et al., 2018), and understanding the biological impacts for organisms and ecosystem function and services (e.g., Smale et al., 2019). By using sea surface temperature percentiles, temperature anomalies can be quantified based on their local variability and account for the broad range of temperature regimes in different marine environments. For temperatures exceeding a 90th-percentile threshold beyond a period of 5-days, marine heatwaves can be classified into categories based on their intensity (Hobday et al., 2018). While these recent advances have provided the framework for understanding key aspects of marine heatwaves, a challenge lies ahead for effective integration of physical and biological knowledge for prediction of marine heatwaves and their ecological impacts. This Research Topic is motivated by the need to understand the mechanisms for how marine heatwaves develop and the biological responses to thermal stress events. This Research Topic is a collection of 18 research articles and three review articles aimed at advancing our knowledge of marine heatwaves within four themes. These themes include methods for detecting marine heatwaves, understanding their physical mechanisms, seasonal forecasting and climate projections, and ecological impacts.
    Description: We thank the contributing authors, reviewers, and the editorial staff at Frontiers in Marine Science for their support in producing this issue. We thank the Marine Heatwaves Working Group (http://www.marineheatwaves.org/) for inspiration and discussions. This special issue stemmed from the session on Advances in Understanding Marine Heat Waves and Their Impacts at the 2018 Ocean Sciences meeting (Portland, USA).
    Keywords: Marine heatwaves ; Extreme events ; Ocean and atmosphere interactions ; Marine ecosystems ; Marine resources ; Climate change ; Climate variability ; Climate prediction
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  • 23
    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Gewirtzman, J., Tang, J., Melillo, J. M., Werner, W. J., Kurtz, A. C., Fulweiler, R. W., & Carey, J. C. Soil warming accelerates biogeochemical silica cycling in a temperate forest. Frontiers in Plant Science, 10, (2019): 1097, doi:10.3389/fpls.2019.01097.
    Description: Biological cycling of silica plays an important role in terrestrial primary production. Soil warming stemming from climate change can alter the cycling of elements, such as carbon and nitrogen, in forested ecosystems. However, the effects of soil warming on the biogeochemical cycle of silica in forested ecosystems remain unexplored. Here we examine long-term forest silica cycling under ambient and warmed conditions over a 15-year period of experimental soil warming at Harvard Forest (Petersham, MA). Specifically, we measured silica concentrations in organic and mineral soils, and in the foliage and litter of two dominant species (Acer rubrum and Quercus rubra), in a large (30 × 30 m) heated plot and an adjacent control plot (30 × 30 m). In 2016, we also examined effects of heating on dissolved silica in the soil solution, and conducted a litter decomposition experiment using four tree species (Acer rubrum, Quercus rubra, Betula lenta, Tsuga canadensis) to examine effects of warming on the release of biogenic silica (BSi) from plants to soils. We find that tree foliage maintained constant silica concentrations in the control and warmed plots, which, coupled with productivity enhancements under warming, led to an increase in total plant silica uptake. We also find that warming drove an acceleration in the release of silica from decaying litter in three of the four species we examined, and a substantial increase in the silica dissolved in soil solution. However, we observe no changes in soil BSi stocks with warming. Together, our data indicate that warming increases the magnitude of silica uptake by vegetation and accelerates the internal cycling of silica in in temperate forests, with possible, and yet unresolved, effects on the delivery of silica from terrestrial to marine systems.
    Description: This research was supported by the National Science Foundation (NSF PLR-1417763 to JT), the Geological Society of America (Stephen G. Pollock Undergraduate Research Grant to JG), the Institute at Brown for Environment and Society, and the Marine Biological Laboratory. Sample analysis and Fulweiler’s involvement were supported by Boston University and a Bullard Fellowship from Harvard University. The soil warming experiment was supported by the National Science Foundation (DEB-0620443) and Department of Energy (DE-FC02-06-ER641577 and DE-SC0005421).
    Keywords: Silica ; Climate change ; Soil ; Warming ; Phytoliths ; Plants ; Biogeochemistry
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  • 24
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Turk, D., Wang, H., Hu, X., Gledhill, D. K., Wang, Z. A., Jiang, L., & Cai, W. Time of Emergence of surface ocean carbon dioxide trends in the North American coastal margins in support of ocean acidification observing system design. Frontiers in Marine Science, 6, (2019):91, doi:10.3389/fmars.2019.00091.
    Description: Time of Emergence (ToE) is the time when a signal emerges from the noise of natural variability. Commonly used in climate science for the detection of anthropogenic forcing, this concept has recently been applied to geochemical variables, to assess the emerging times of anthropogenic ocean acidification (OA), mostly in the open ocean using global climate and Earth System Models. Yet studies of OA variables are scarce within costal margins, due to limited multidecadal time-series observations of carbon parameters. ToE provides important information for decision making regarding the strategic configuration of observing assets, to ensure they are optimally positioned either for signal detection and/or process elicitation and to identify the most suitable variables in discerning OA-related changes. Herein, we present a short overview of ToE estimates on an OA variable, CO2 fugacity f(CO2,sw), in the North American ocean margins, using coastal data from the Surface Ocean CO2 Atlas (SOCAT) V5. ToE suggests an average theoretical timeframe for an OA signal to emerge, of 23(±13) years, but with considerable spatial variability. Most coastal areas are experiencing additional secular and/or multi-decadal forcing(s) that modifies the OA signal, and such forcing may not be sufficiently resolved by current observations. We provide recommendations, which will help scientists and decision makers design and implement OA monitoring systems in the next decade, to address the objectives of OceanObs19 (http://www.oceanobs19.net) in support of the United Nations Decade of Ocean Science for Sustainable Development (2021–2030) (https://en.unesco.org/ocean-decade) and the Sustainable Development Goal (SDG) 14.3 (https://sustainabledevelopment.un.org/sdg14) target to “Minimize and address the impacts of OA.”
    Description: HW was partially supported by an NSF grant (OCE#1654232) while being a research associate at TAMUCC.
    Keywords: Ocean acidification ; CO2 fugacity ; Time of emergence ; Climate change ; Novel statistical approaches ; Observing system optimization ; Decision making tool
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  • 25
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Palmer, M. D., Durack, P. J., Paz Chidichimo, M., Church, J. A., Cravatte, S., Hill, K., Johannessen, J. A., Karstensen, J., Lee, T., Legler, D., Mazloff, M., Oka, E., Purkey, S., Rabe, B., Sallee, J., Sloyan, B. M., Speich, S., von Schuckmann, K., Willis, J., & Wijffels, S. Adequacy of the ocean observation system for quantifying regional heat and freshwater storage and change. Frontiers in Marine Science, 6, (2019): 16, doi: 10.3389/fmars.2019.00416.
    Description: Considerable advances in the global ocean observing system over the last two decades offers an opportunity to provide more quantitative information on changes in heat and freshwater storage. Variations in these storage terms can arise through internal variability and also the response of the ocean to anthropogenic climate change. Disentangling these competing influences on the regional patterns of change and elucidating their governing processes remains an outstanding scientific challenge. This challenge is compounded by instrumental and sampling uncertainties. The combined use of ocean observations and model simulations is the most viable method to assess the forced signal from noise and ascertain the primary drivers of variability and change. Moreover, this approach offers the potential for improved seasonal-to-decadal predictions and the possibility to develop powerful multi-variate constraints on climate model future projections. Regional heat storage changes dominate the steric contribution to sea level rise over most of the ocean and are vital to understanding both global and regional heat budgets. Variations in regional freshwater storage are particularly relevant to our understanding of changes in the hydrological cycle and can potentially be used to verify local ocean mass addition from terrestrial and cryospheric systems associated with contemporary sea level rise. This White Paper will examine the ability of the current ocean observing system to quantify changes in regional heat and freshwater storage. In particular we will seek to answer the question: What time and space scales are currently resolved in different regions of the global oceans? In light of some of the key scientific questions, we will discuss the requirements for measurement accuracy, sampling, and coverage as well as the synergies that can be leveraged by more comprehensively analyzing the multi-variable arrays provided by the integrated observing system.
    Description: MP was supported by the Met Office Hadley Centre Climate Programme funded by the BEIS and Defra, and the European Union’s Horizon 2020 Research and Innovation Program under grant Agreement No. 633211 (AtlantOS). The work of PD was prepared the by Lawrence Livermore National Laboratory (LLNL) under Contract DE-AC52-07NA27344 and is a contribution to the U.S. Department of Energy, Office of Science, Climate and Environmental Sciences Division, Regional and Global Modeling and Analysis Program. LLNL Release number: LLNL-JRNL-761158. BS and JC was partially supported by the Centre for Southern Hemisphere Oceans Research, a joint research center between the QNLM and the CSIRO. BS was also supported by the Australian Government Department of the Environment and CSIRO through the National Environmental Science Program. SC was supported by the IRD and by the French national program LEFE/INSU. SC thanks W. Kessler for suggestions concerning Figure 6. BR was supported by the German Alfred-Wegener-Institut Helmholtz-Zentrum für Polar-und Meeresforschung (AWI). J-BS was supported by the CNRS/INSU and the Horizon 2020 Research and Innovation Program under Grant Agreement 637770. SS was supported by the French Institutions ENS, LMD, IPSL, and CNRS/INSU. The work of JW was performed in part at the Jet Propulsion Laboratory, California Institute of Technology, under contract with the National Aeronautics and Space Administration.
    Keywords: Heat content ; Freshwater content ; Salinity ; Temperature ; Ocean observing system ; Climate change ; Climate variability ; Observing system design
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  • 26
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in O'Brien, F. J. M., Almaraz, M., Foster, M. A., Hill, A. F., Huber, D. P., King, E. K., Langford, H., Lowe, M., Mickan, B. S., Miller, V. S., Moore, O. W., Mathes, F., Gleeson, D., & Leopold, M. Soil salinity and pH drive soil bacterial community composition and diversity along a lateritic slope in the Avon River critical zone observatory, Western Australia. Frontiers in Microbiology, 10, (2019): 1486, doi:10.3389/fmicb.2019.01486.
    Description: Soils are crucial in regulating ecosystem processes, such as nutrient cycling, and supporting plant growth. To a large extent, these functions are carried out by highly diverse and dynamic soil microbiomes that are in turn governed by numerous environmental factors including weathering profile and vegetation. In this study, we investigate geophysical and vegetation effects on the microbial communities of iron-rich lateritic soils in the highly weathered landscapes of Western Australia (WA). The study site was a lateritic hillslope in southwestern Australia, where gradual erosion of the duricrust has resulted in the exposure of the different weathering zones. High-throughput amplicon sequencing of the 16S rRNA gene was used to investigate soil bacterial community diversity, composition and functioning. We predicted that shifts in the microbial community would reflect variations in certain edaphic properties associated with the different layers of the lateritic profile and vegetation cover. Our results supported this hypothesis, with electrical conductivity, pH and clay content having the strongest correlation with beta diversity, and many of the differentially abundant taxa belonging to the phyla Actinobacteria and Proteobacteria. Soil water repellence, which is associated with Eucalyptus vegetation, also affected beta diversity. This enhanced understanding of the natural system could help to improve future crop management in WA since the physicochemical properties of the agricultural soils in this region are inherited from laterites via the weathering and pedogenesis processes.
    Description: This work was funded by the WUN and the individual authors’ institutions. MA and MF were funded by the Critical Zone Observatory Program, NSF ICER 1445346.
    Keywords: Soil microbial ; Community ; Bacteria ; Laterite ; Critical zone ; Western Australia
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  • 27
    Publication Date: 2022-10-26
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Seyler, L. M., Tuorto, S., McGuinness, L. R., Gong, D., & Kerkhof, L. J. Bacterial and archaeal specific-predation in the North Atlantic Basin. Frontiers in Marine Science, 6, (2019): 555, doi:10.3389/fmars.2019.00555.
    Description: Stable isotope probing (SIP) was used to track prokaryotic and eukaryotic carbon uptake along a meridional transect (Long. 52°W) in the North Atlantic to assess if 13C-resource partitioning between bacteria and archaea and 13C-labeled eukaryotic predators could be detected. One-liter SIP microcosms were amended with 13C-acetate or 13C-urea and incubated for 48 h. Our data indicated archaea often outcompeted bacteria for 13C-urea while both archaea and bacteria could incorporate 13C-acetate. This 13C label could also be tracked into eukaryotic microbes. The largest number of 13C-labeled eukaryotic OTUs, and the greatest percentage of eukaryotic 13C signal, were observed in conjunction with both archaeal and bacterial 13C incorporation, suggesting that most eukaryotic predators do not distinguish between archaeal and bacterial prey. However, other 13C-eukaryotic OTUs were exclusively associated with either 13C-archaeal or 13C-bacterial OTUs. These archaeal-specific and bacterial-specific 13C-eukaryotic OTUs were related to known bactivorous predators including Ancyromonas, Amastigomonas, Cafeteria, and Caecitellus. Our SIP findings suggest both resource partitioning between bacteria and TACK (Thaumarchaeota, Aigarchaeota, Crenarchaeota, and Korarchaeota) archaea and selective predation by eukaryotic predators. Determining the equalizing mechanisms for co-existence in the marine environment can help map predator/prey interactions to better estimate carbon flow in the deep ocean.
    Description: This research was made possible through the support of the U.S Global Ocean Carbon and Repeat Hydrography Program and NSF Ocean Technology and Interdisciplinary Program grant (#1131022) to LK.
    Keywords: Archaea ; Bacteria ; Predation ; Competition ; Stable isotope probing ; Deep ocean
    Repository Name: Woods Hole Open Access Server
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  • 28
    Publication Date: 2022-05-26
    Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 7 (2016): 941, doi:10.3389/fmicb.2016.00941.
    Description: Pockmarks are crater-like depression on the seafloor associated with hydrocarbon ascent through muddy sediments in continental shelves around the world. In this study, we examine the diversity and distribution of benthic microbial communities at shallow-water pockmarks adjacent to the Middle Adriatic Ridge. We integrate microbial diversity data with characterization of local hydrocarbons concentrations and sediment geochemistry. Our results suggest these pockmarks are enriched in sedimentary hydrocarbons, and host a microbial community dominated by Bacteria, even in deeper sediment layers. Pockmark sediments showed higher prokaryotic abundance and biomass than surrounding sediments, potentially due to the increased availability of organic matter and higher concentrations of hydrocarbons linked to pockmark activity. Prokaryotic diversity analyses showed that the microbial communities of these shallow-water pockmarks are unique, and comprised phylotypes associated with the cycling of sulfur and nitrate compounds, as well as numerous know hydrocarbon degraders. Altogether, this study suggests that shallow-water pockmark habitats enhance the diversity of the benthic prokaryotic biosphere by providing specialized environmental niches.
    Description: This work was partially supported by a Postdoctoral Fellowship from the Center for Dark Energy Biosphere Investigations [C-DEBI, grant OCE-0939564] awarded to DG, by National Science Foundation grant OCE 11-24141 to CV, and European Science Foundation EuroDeep BIOFUN grant CTM2007-28739-E to EM. This article commits to EU HERMIONE [contract no. 226354] and CoCoNet [contract no. 287844] programs, and the Italian MIUR flag Ritmare within the National Research Program 2011–2013.
    Keywords: Pockmarks ; Cold seeps ; Hydrocarbons ; Prokaryotic diversity ; Bacteria ; Archaea ; Hydrocarbon degradation ; Microbial diversity
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  • 29
    Publication Date: 2022-05-25
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 5 (2014): 647, doi:10.3389/fmicb.2014.00647.
    Description: The Southern Ocean is currently subject to intense investigations, mainly related to its importance for global biogeochemical cycles and its alarming rate of warming in response to climate change. Microbes play an essential role in the functioning of this ecosystem and are the main drivers of the biogeochemical cycling of elements. Yet, the diversity and abundance of microorganisms in this system remain poorly studied, in particular with regards to changes along environmental gradients. Here, we used amplicon sequencing of 16S rRNA gene tags using primers covering both Bacteria and Archaea to assess the composition and diversity of the microbial communities from four sampling depths (surface, the maximum and minimum of the oxygen concentration, and near the seafloor) at 10 oceanographic stations located in Bransfield Strait [northwest of the Antarctic Peninsula (AP)] and near the sea ice edge (north of the AP). Samples collected near the seafloor and at the oxygen minimum exhibited a higher diversity than those from the surface and oxygen maximum for both bacterial and archaeal communities. The main taxonomic groups identified below 100 m were Thaumarchaeota, Euryarchaeota and Proteobacteria (Gamma-, Delta-, Beta-, and Alphaproteobacteria), whereas in the mixed layer above 100 m Bacteroidetes and Proteobacteria (mainly Alpha- and Gammaproteobacteria) were found to be dominant. A combination of environmental factors seems to influence the microbial community composition. Our results help to understand how the dynamic seascape of the Southern Ocean shapes the microbial community composition and set a baseline for upcoming studies to evaluate the response of this ecosystem to future changes.
    Description: This work was supported by the Brazilian National Counsel of Technological and Scientific Development (Polar Canion CNPq 556848/2009-8, ProOasis CNPq 565040/2010-3, Interbiota CNPq 407889/2013-2 and INCT-MAR-COI). Alex Enrich-Prast received a CNPq Productivity fellowship. Camila N. Signori was supported by a WHOI Mary Sears Visitor Award (for the microbial community analyses) and by the Brazilian Federal Agency for Support and Evaluation of Graduate Education (CAPES) for the “Doctorate Sandwich” scholarship (n. 18835/12-0).
    Keywords: Antarctica ; Pyrosequencing ; Microbial community structure ; Environmental factors ; Microbial oceanography ; Climate change
    Repository Name: Woods Hole Open Access Server
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  • 30
    Publication Date: 2022-05-25
    Description: © The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Frontiers in Microbiology 6 (2015): 104, doi:10.3389/fmicb.2015.00104.
    Description: Soil microbes are major drivers of soil carbon cycling, yet we lack an understanding of how climate warming will affect microbial communities. Three ongoing field studies at the Harvard Forest Long-term Ecological Research (LTER) site (Petersham, MA) have warmed soils 5°C above ambient temperatures for 5, 8, and 20 years. We used this chronosequence to test the hypothesis that soil microbial communities have changed in response to chronic warming. Bacterial community composition was studied using Illumina sequencing of the 16S ribosomal RNA gene, and bacterial and fungal abundance were assessed using quantitative PCR. Only the 20-year warmed site exhibited significant change in bacterial community structure in the organic soil horizon, with no significant changes in the mineral soil. The dominant taxa, abundant at 0.1% or greater, represented 0.3% of the richness but nearly 50% of the observations (sequences). Individual members of the Actinobacteria, Alphaproteobacteria and Acidobacteria showed strong warming responses, with one Actinomycete decreasing from 4.5 to 1% relative abundance with warming. Ribosomal RNA copy number can obfuscate community profiles, but is also correlated with maximum growth rate or trophic strategy among bacteria. Ribosomal RNA copy number correction did not affect community profiles, but rRNA copy number was significantly decreased in warming plots compared to controls. Increased bacterial evenness, shifting beta diversity, decreased fungal abundance and increased abundance of bacteria with low rRNA operon copy number, including Alphaproteobacteria and Acidobacteria, together suggest that more or alternative niche space is being created over the course of long-term warming.
    Description: This work was supported by funding from the University of Massachusetts Amherst to DeAngelis and the National Science Foundation Long-term Ecological Research (LTER) Program.
    Keywords: Climate change ; Microbial ecology ; Ribosomal RNA ; rrn operon copy number ; Trophic strategy
    Repository Name: Woods Hole Open Access Server
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  • 31
    Publication Date: 2022-05-26
    Description: © The Author(s), 2011. This is an open-access article subject to a non-exclusive license between the authors and Frontiers Media SA, which permits use, distribution and reproduction in other forums. The definitive version was published in Frontiers in Microbiology 2 (2011): 160, doi:10.3389/fmicb.2011.00160.
    Description: The Ross Sea is home to some of the largest phytoplankton blooms in the Southern Ocean. Primary production in this system has previously been shown to be iron limited in the summer and periodically iron and vitamin B12 colimited. In this study, we examined trace metal limitation of biological activity in the Ross Sea in the austral spring and considered possible implications for vitamin B12 nutrition. Bottle incubation experiments demonstrated that iron limited phytoplankton growth in the austral spring while B12, cobalt, and zinc did not. This is the first demonstration of iron limitation in a Phaeocystis antarctica-dominated, early season Ross Sea phytoplankton community. The lack of B12 limitation in this location is consistent with previous Ross Sea studies in the austral summer, wherein vitamin additions did not stimulate P. antarctica growth and B12 was limiting only when bacterial abundance was low. Bottle incubation experiments and a bacterial regrowth experiment also revealed that iron addition directly enhanced bacterial growth. B12 uptake measurements in natural water samples and in an iron fertilized bottle incubation demonstrated that bacteria serve not only as a source for vitamin B12, but also as a significant sink, and that iron additions enhanced B12 uptake rates in phytoplankton but not bacteria. Additionally, vitamin uptake rates did not become saturated upon the addition of up to 95 pM B12. A rapid B12 uptake rate was observed after 13 min, which then decreased to a slower constant uptake rate over the next 52 h. Results from this study highlight the importance of iron availability in limiting early season Ross Sea phytoplankton growth and suggest that rates of vitamin B12 production and consumption may be impacted by iron availability.
    Description: This research was supported by NSF grants OCE-0752291, OPP-0440840, OPP-0338097, OPP-0338164, ANT-0732665, OCE-0452883, and OCE-1031271, the Center for Microbial Oceanography Research and Education (CMORE) and a National Science Foundation (NSF) Graduate Research Fellowship (2007037200) and an Environmental Protection Agency STAR Fellowship to EMB (F6E20324).
    Keywords: Iron limitation ; Vitamin B12 ; Ross Sea ; Colimitation ; Bacteria ; Phytoplankton ; Iron fertilization
    Repository Name: Woods Hole Open Access Server
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  • 32
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Scientific Reports 2 (2012): 553, doi:10.1038/srep00553.
    Description: Sea surface temperature imagery, satellite altimetry, and a surface drifter track reveal an unusual tilt in the Gulf Stream path that brought the Gulf Stream to 39.9°N near the Middle Atlantic Bight shelfbreak—200 km north of its mean position—in October 2011, while a large meander brought Gulf Stream water within 12 km of the shelfbreak in December 2011. Near-bottom temperature measurements from lobster traps on the outer continental shelf south of New England show distinct warming events (temperature increases exceeding 6°C) in November and December 2011. Moored profiler measurements over the continental slope show high salinities and temperatures, suggesting that the warm water on the continental shelf originated in the Gulf Stream. The combination of unusual water properties over the shelf and slope in late fall and the subsequent mild winter may affect seasonal stratification and habitat selection for marine life over the continental shelf in 2012.
    Description: Profiler data were made available by the Ocean Observatory Initiative (OOI) during the construction phase of the project. The OOI is funded by the National Science Foundation and managed by the Consortium for Ocean Leadership. Drifter data were provided by Tim Shaw and David Calhoun at Cape Fear Community College.GGGwas supported by NSFGrant OCE-1129125. RET was supported by the Postdoctoral Scholar Program at the Woods Hole Oceanographic Institution, with funding provided by the Cooperative Institute for the North Atlantic Region. MA was supported by the Penzance Endowed Fund in Support of Assistant Scientists.
    Keywords: Ecology ; Climate change ; Atmospheric science ; Oceanography
    Repository Name: Woods Hole Open Access Server
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