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Long-term forest soil warming alters microbial communities in temperate forest soils (2015)

DeAngelis, Kristen M. ; Pold, Grace ; Topcuoglu, Begum D. ; [et al.]

Frontiers Media

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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

Type: Article

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Long-term warming alters carbohydrate degradation potential in temperate forest soils (2016)

Pold, Grace ; Billings, Andrew F. ; Blanchard, Jeffrey L. ; [et al.]

American Society for Microbiology

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Publication Date: 2022-05-25

Description: © The Author(s), 2016. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Applied and Environmental Microbiology 82 (2016): 6518-6530, doi:10.1128/AEM.02012-16.

Description: As Earth's climate warms, soil carbon pools and the microbial communities that process them may change, altering the way in which carbon is recycled in soil. In this study, we used a combination of metagenomics and bacterial cultivation to evaluate the hypothesis that experimentally raising soil temperatures by 5°C for 5, 8, or 20 years increased the potential for temperate forest soil microbial communities to degrade carbohydrates. Warming decreased the proportion of carbohydrate-degrading genes in the organic horizon derived from eukaryotes and increased the fraction of genes in the mineral soil associated with Actinobacteria in all studies. Genes associated with carbohydrate degradation increased in the organic horizon after 5 years of warming but had decreased in the organic horizon after warming the soil continuously for 20 years. However, a greater proportion of the 295 bacteria from 6 phyla (10 classes, 14 orders, and 34 families) isolated from heated plots in the 20-year experiment were able to depolymerize cellulose and xylan than bacterial isolates from control soils. Together, these findings indicate that the enrichment of bacteria capable of degrading carbohydrates could be important for accelerated carbon cycling in a warmer world.

Description: This work, including the efforts of Jeffrey Blanchard, Serita D. Frey, Jerry M. Melillo, and Kristen M. DeAngelis, was funded by National Science Foundation (NSF) (NSF 1237491, NSF 1456528, and ACI-1053575). This work, including the efforts of Jeffrey Blanchard, Serita D. Frey, Jerry M. Melillo, Linda T. A. van Diepen, and Kristen M. DeAngelis, was funded by U.S. Department of Energy (DOE) (DE-AC02-05CH11231). This work, including the efforts of Grace Pold, Andrew F. Billings, Jeffrey Blanchard, Jerry M. Melillo, and Kristen M. DeAngelis, was funded by U.S. Department of Energy (DOE) (DE-SC0010740).

Repository Name: Woods Hole Open Access Server

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Fungal community response to long-term soil warming with potential implications for soil carbon dynamics (2021)

Pec, Gregory J. ; van Diepen, Linda T. A. ; Knorr, Melissa ; [et al.]

Ecological Society of America

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Publication Date: 2022-10-27

Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Pec, G. J., van Diepen, L. T. A., Knorr, M., Grandy, A. S., Melillo, J. M., DeAngelis, K. M., Blanchard, J. L., & Frey, S. D. Fungal community response to long-term soil warming with potential implications for soil carbon dynamics. Ecosphere, 12(5), (2021): e03460, https://doi.org/10.1002/ecs2.3460.

Description: The direction and magnitude of climate warming effects on ecosystem processes such as carbon cycling remain uncertain. Soil fungi are central to these processes due to their roles as decomposers of soil organic matter, as mycorrhizal symbionts, and as determinants of plant diversity. Yet despite their importance to ecosystem functioning, we lack a clear understanding of the long-term response of soil fungal communities to warming. Toward this goal, we characterized soil fungal communities in two replicated soil warming experiments at the Harvard Forest (Petersham, Massachusetts, USA) which had experienced 5°C above ambient soil temperatures for 5 and 20 yr at the time of sampling. We assessed fungal diversity and community composition by sequencing the ITS2 region of rDNA using Illumina technology, along with soil C concentrations and chemistry. Three main findings emerged: (1) long-, but not short-term warming resulted in compositional shifts in the soil fungal community, particularly in the saprotrophic and unknown components of the community; (2) soil C concentrations and the total C stored in the organic horizon declined in response to both short- (5 yr) and long-term (20 yr) warming; and (3) following long-term warming, shifts in fungal guild relative abundances were associated with substantial changes in soil organic matter chemistry, particularly the relative abundance of lignin. Taken together, our results suggest that shifts with warming in the relative abundance of fungal functional groups and dominant fungal taxa are related to observed losses in total soil C.

Description: NSF Long-term Research in Environmental Biology. Grant Number: DEB 1456528 NSF Long-term Ecological Research. Grant Number: DEB 1237491 Joint Genome Institute as part of a Community Sequencing Program Award. Grant Number: DE-AC02-05CH11231 CSP-1058

Keywords: Ectomycorrhizal fungi ; Illumina ; Organic matter chemistry ; Saprotrophic fungi ; Soil carbon

Repository Name: Woods Hole Open Access Server

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The transcriptional response of soil bacteria to long-term warming and short-term seasonal fluctuations in a terrestrial forest (2022)

Chowdhury, Priyanka Roy ; Golas, Stefan M. ; Alteio, Lauren V. ; [et al.]

Frontiers Media

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Publication Date: 2022-10-27

Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Chowdhury, P. R., Golas, S. M., Alteio, L., Stevens, J. T. E., Billings, A. F., Blanchard, J. L., Melillo, J. M., & DeAngelis, K. M. The transcriptional response of soil bacteria to long-term warming and short-term seasonal fluctuations in a terrestrial forest. Frontiers in Microbiology, 12, (2021): 666558, https://doi.org/10.3389/fmicb.2021.666558.

Description: Terrestrial ecosystems are an important carbon store, and this carbon is vulnerable to microbial degradation with climate warming. After 30 years of experimental warming, carbon stocks in a temperate mixed deciduous forest were observed to be reduced by 30% in the heated plots relative to the controls. In addition, soil respiration was seasonal, as was the warming treatment effect. We therefore hypothesized that long-term warming will have higher expressions of genes related to carbohydrate and lipid metabolism due to increased utilization of recalcitrant carbon pools compared to controls. Because of the seasonal effect of soil respiration and the warming treatment, we further hypothesized that these patterns will be seasonal. We used RNA sequencing to show how the microbial community responds to long-term warming (~30 years) in Harvard Forest, MA. Total RNA was extracted from mineral and organic soil types from two treatment plots (+5°C heated and ambient control), at two time points (June and October) and sequenced using Illumina NextSeq technology. Treatment had a larger effect size on KEGG annotated transcripts than on CAZymes, while soil types more strongly affected CAZymes than KEGG annotated transcripts, though effect sizes overall were small. Although, warming showed a small effect on overall CAZymes expression, several carbohydrate-associated enzymes showed increased expression in heated soils (~68% of all differentially expressed transcripts). Further, exploratory analysis using an unconstrained method showed increased abundances of enzymes related to polysaccharide and lipid metabolism and decomposition in heated soils. Compared to long-term warming, we detected a relatively small effect of seasonal variation on community gene expression. Together, these results indicate that the higher carbohydrate degrading potential of bacteria in heated plots can possibly accelerate a self-reinforcing carbon cycle-temperature feedback in a warming climate.

Description: Funding for this study was provided by the Department of Energy Terrestrial Ecosystem Sciences program under contract number DE-SC0010740. Sites for sample collection were maintained with funding in part from the National Science Foundation (NSF) Long-Term Ecological Research (DEB 1237491) and the NSF Long-Term Research in Environmental Biology (DEB 1456528) programs.

Keywords: Meta-transcriptomes ; Microbial ; Terrestrial ; Carbon cycle ; Global warming

Repository Name: Woods Hole Open Access Server

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5

Electronic Resource

The Non-Photosynthetic Plastid in Malarial Parasites and Other Apicomplexans is Derived from Outside the Green Plastid Lineage (1999)

BLANCHARD, JEFFREY L. ; HICKS, JUSTIN S.

Oxford, UK : Blackwell Publishing Ltd

The @journal of eukaryotic microbiology 46 (1999), S. 0

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ISSN: 1550-7408

Source: Blackwell Publishing Journal Backfiles 1879-2005

Topics: Biology

Notes: The discovery of a non-photosynthetic plastid genome in Plasmodium falciparum and other apicomplexans has provided a new drug target, but the evolutionary origin of the plastid has been muddled by the lack of characters, that typically define major plastid lineages. To clarify the ancestry of the plastid, we undertook a comprehensive analysis of all genomic characters shared by completely sequenced plastid genomes. Cladistic analysis of the pattern of plastid gene loss and gene rearrangements suggests that the apicomplexan plastid is derived from an ancestor outside of the green plastid lineage. Phylogenetic analysis of primary sequence data (DNA and amino acid characters) produces results that are generally independent of the analytical method, but similar genes (i.e. rpoB and rpoC) give similar topologies. The conflicting phylogenies in primary sequence data sets make it difficult to determine the exact origin of the apicomplexan plastid and the apparent artifactual association of apicomplexan and euglenoid sequences suggests that DNA sequence data may be an inappropriate set of characters to address this phylogenetic question. At present we cannot reject our null hypothesis that the apicomplexan plastid is derived from a shared common ancestor between apicomplexans and dinoflagellates. During the analysis, we noticed that the Plasmodium tRNA-Met is probably tRNA-fMet and the tRNA-fMet is probably tRNA-Ile. We suggest that P. falciparum has lost the elongator type tRNA-Met and that similar to metazoan mitochondria there is only one species of methionine tRNA. In P. falciparum, this has been accomplished by recruiting the fMet-type tRNA to dually function in initiation and elongation. The tRNA-Ile has an unusual stem-loop in the variable region. The insertion in this region appears to have occurred after the primary origin of the plastid and further supports the monophyletic ancestory of plastids.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1111/j.1550-7408.1999.tb04615.x

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Electronic Resource

Pervasive migration of organellar DNA to the nucleus in plants (1995)

Blanchard, Jeffrey L. ; Schmidt, Gregory W.

Springer

Journal of molecular evolution 41 (1995), S. 397-406

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ISSN: 1432-1432

Keywords: Chloroplast ; Mitochondrion ; Nucleus ; Gene transfer ; DNA migration ; mRNA ; editing ; Illegitimate recombination ; Nonhomologous recombination ; Random integration ; End joining ; Genomic evolution

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract A surprisingly large number of plant nuclear DNA sequences inferred to be remnants of chloroplast and mitochondrial DNA migration events were detected through computer-assisted database searches. Nineteen independent organellar DNA insertions, with a median size of 117 by (range of 38 to 〉785 bp), occur in the proximity of 15 nuclear genes. One fragment appears to have been passed through a RNA intermediate, based on the presence of an edited version of the mitochondrial gene in the nucleus. Tandemly arranged fragments from disparate regions of organellar genomes and from different organellar genomes indicate that the fragments joined together from an intracellular pool of RNA and/or DNA before they integrated into the nuclear genome. Comparisons of integrated sequences to genes lacking the insertions, as well as the occurrence of coligated fragments, support a model of random integration by end joining. All transferred sequences were found in noncoding regions, but the positioning of organellar-derived DNA in introns, as well as regions 5′ and 3′ to nuclear genes, suggests that the random integration of organellar DNA has the potential to influence gene expression patterns. A semiquantitative estimate was performed on the amount of organellar DNA being transferred and assimilated into the nucleus. Based on this database survey, we estimate that 3–7% of the plant nuclear genomic sequence files contain organellar-derived DNA. The timing and the magnitude of genetic flux to the nuclear genome suggest that random integration is a substantial and ongoing process for creating sequence variation.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1007/BF00160310

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Electronic Resource

Deleterious mutation accumulation in organelle genomes (1998)

Lynch, Michael ; Blanchard, Jeffrey L.

Springer

Genetica 102-103 (1998), S. 29-39

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ISSN: 1573-6857

Keywords: chloroplast genome ; deleterious mutation ; mitochondrial genome ; Muller's ratchet ; ribosomal RNA ; transfer RNA

Source: Springer Online Journal Archives 1860-2000

Topics: Biology

Notes: Abstract It is well established on theoretical grounds that the accumulation of mildly deleterious mutations in nonrecombining genomes is a major extinction risk in obligately asexual populations. Sexual populations can also incur mutational deterioration in genomic regions that experience little or no recombination, i.e., autosomal regions near centromeres, Y chromosomes, and organelle genomes. Our results suggest, for a wide array of genes (transfer RNAs, ribosomal RNAs, and proteins) in a diverse collection of species (animals, plants, and fungi), an almost universal increase in the fixation probabilities of mildly deleterious mutations arising in mitochondrial and chloroplast genomes relative to those arising in the recombining nuclear genome. This enhanced width of the selective sieve in organelle genomes does not appear to be a consequence of relaxed selection, but can be explained by the decline in the efficiency of selection that results from the reduction of effective population size induced by uniparental inheritance. Because of the very low mutation rates of organelle genomes (on the order of 10-4 per genome per year), the reduction in fitness resulting from mutation accumulation in such genomes is a very long-term process, not likely to imperil many species on time scales of less than a million years, but perhaps playing some role in phylogenetic lineage sorting on time scales of 10 to 100 million years.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1023/A:1017022522486

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