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1. Strong Dispersal Limitation of Microbial Communities at Shackleton Glacier, Antarctica

   https://doi.org/10.1128/msystems.01254-22  

   Lemoine, Nathan P. ; Adams, Byron J. ; Diaz, Melisa ; Dragone, Nicholas B. ; Franco, André L. ; Fierer, Noah ; Lyons, W. Berry ; Hogg, Ian D. ; Wall, Diana H. ( February 2023 , mSystems)

   Lurgi, Miguel (Ed.)

   ABSTRACT Microbial communities can be structured by both deterministic and stochastic processes, but the relative importance of these processes remains unknown. The ambiguity partly arises from an inability to disentangle soil microbial processes from confounding factors, such as aboveground plant communities or anthropogenic disturbance. In this study, we characterized the relative contributions of determinism and stochasticity to assembly processes of soil bacterial communities across a large environmental gradient of undisturbed Antarctic soils. We hypothesized that harsh soils would impose a strong environmental selection on microbial communities, whereas communities in benign soils would be structured largely by dispersal. Contrary to our expectations, dispersal was the dominant assembly mechanism across the entire soil environmental gradient, including benign environments. The microbial community composition reflects slowly changing soil conditions and dispersal limitation of isolated sites. Thus, stochastic processes, as opposed to deterministic, are primary drivers of soil ecosystem assembly across space at our study site. This is especially surprising given the strong environmental constraints on soil microorganisms in one of the harshest environments on the planet, suggesting that dispersal could be a driving force in microbial community assembly in soils worldwide. IMPORTANCE Because of their diversity and ubiquity, microbes provide an excellent means to tease apart how natural communities are structured. In general, ecologists believe that stochastic assembly processes, like random drift and dispersal, should dominate in benign environments while deterministic processes, like environmental filtering, should be prevalent in harsh environments. To help resolve this debate, we analyzed microbial community composition in pristine Antarctic soils devoid of human influence or plant communities for eons. Our results demonstrate that dispersal limitation is a surprisingly potent force of community limitation throughout all soil conditions. Thus, dispersal appears to be a driving force of microbial community assembly, even in the harshest of conditions. 

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2. Fungal infection alters the selection, dispersal and drift processes structuring the amphibian skin microbiome

   https://doi.org/10.1111/ele.13414  

   Wilber, Mark Q. ; Jani, Andrea J. ; Mihaljevic, Joseph R. ; Briggs, Cheryl J. ; Shade, ed., Ashley ( October 2019 , Ecology Letters)

   Symbiotic microbial communities are important for host health, but the processes shaping these communities are poorly understood. Understanding how community assembly processes jointly affect microbial community composition is limited because inflexible community models rely on rejecting dispersal and drift before considering selection. We developed a flexible community assembly model based on neutral theory to ask: How do dispersal, drift and selection concurrently affect the microbiome across environmental gradients? We applied this approach to examine how a fungal pathogen affected the assembly processes structuring the amphibian skin microbiome. We found that the rejection of neutrality for the amphibian microbiome across a fungal gradient was not strictly due to selection processes, but was also a result of species‐specific changes in dispersal and drift. Our modelling framework brings the qualitative recognition that niche and neutral processes jointly structure microbiomes into quantitative focus, allowing for improved predictions of microbial community turnover across environmental gradients.

    

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3. Historical forest disturbance mediates soil microbial community responses to drought

   https://doi.org/10.1111/1462-2920.15706  

   Osburn, Ernest D. ; Badgley, Brian D. ; Aylward, Frank O. ; Barrett, J. E. ( August 2021 , Environmental Microbiology)

   Despite the abundance of studies demonstrating the effects of drought on soil microbial communities, the role of land use legacies in mediating these drought effects is unclear. To assess historical land use influences on microbial drought responses, we conducted a drought‐rewetting experiment in soils from two adjacent and currently forested watersheds with distinct land use histories: an undisturbed ‘reference’ site and a ‘disturbed’ site that was clear‐cut and converted to agriculture ~60 years prior. We incubated intact soil cores at either constant moisture or under a drought‐rewet treatment and characterized bacterial and fungal communities using amplicon sequencing throughout the experiment. Bacterial alpha diversity decreased following drought‐rewetting while fungal diversity increased. Bacterial beta diversity also changed markedly following drought‐rewetting, especially in historically disturbed soils, while fungal beta diversity exhibited little response. Additionally, bacterial beta diversity in disturbed soils recovered less from drought‐rewetting compared with reference soils. Disturbed soil communities also exhibited notable reductions in nitrifying taxa, increases in putative r‐selected bacteria, and reductions in network connectivity following drought‐rewetting. Overall, our study reveals historical land use to be important in mediating responses of soil bacterial communities to drought, which will influence the ecosystem‐scale trajectories of these environments under ongoing and future climate change.

    

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4. Bacterial community assembly and antibiotic resistance genes in soils exposed to antibiotics at environmentally relevant concentrations

   https://doi.org/10.1111/1462-2920.16371  

   Chen, Zeyou ; Zhang, Wei ; Peng, Anping ; Shen, Yike ; Jin, Xin ; Stedtfeld, Robert D. ; Boyd, Stephen A. ; Teppen, Brian J. ; Tiedje, James M. ; Gu, Cheng ; et al ( March 2023 , Environmental Microbiology)

   Understanding how bacterial community assembly and antibiotic resistance genes (ARGs) respond to antibiotic exposure is essential to deciphering the ecological risk of anthropogenic antibiotic pollution in soils. In this study, three loam soils with different land management (unmanured golf course, dairy‐manured pasture, and swine‐manured cornfield) were spiked with a mixture of 11 antibiotics at the initial concentration of 100 and 1000 μg kg⁻¹for each antibiotic and incubated over 132 days, mimicking a scenario of pulse disturbance and recovery in soils, with unspiked soil samples as the control treatment. The Infer Community Assembly Mechanisms by Phylogenetic‐bin‐based null model (iCAMP) analysis demonstrated that drift and dispersal limitation contributed to 57%–65% and 16%–25%, and homogeneous selection 12%–16% of soil bacterial community assembly. Interestingly, antibiotic exposure to 1000 μg kg⁻¹level significantly increased the contribution of drift to community assembly, largely due to the positive response from Acidobacteria‐6 in the golf course and pasture soils and from Chthoniobacteraceae in the cornfield soil to the antibiotic exposure. However, ARG abundance and diversity in the three soils exhibited antibiotics‐independent temporal fluctuations, but were associated with the changes in soil bacterial communities over time. This study provides the first insight into the relative contributions of different bacterial community assembly processes in soils upon antibiotic exposure at environmentally relevant concentrations.

    

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5. Soil microbiomes in lawns reveal land-use legacy impacts on urban landscapes

   https://doi.org/10.1007/s00442-023-05389-8  

   Thompson, Grant L. ; Bray, Natalie ; Groffman, Peter M. ; Kao-Kniffin, Jenny ( June 2023 , Oecologia)

   Land-use change is highly dynamic globally and there is great uncertainty about the effects of land-use legacies on contemporary environmental performance. We used a chronosequence of urban grasslands (lawns) that were converted from agricultural and forested lands from 10 to over 130 years prior to determine if land-use legacy influences components of soil biodiversity and composition over time. We used historical aerial imagery to identify sites in Baltimore County, MD (USA) with agricultural versus forest land-use history. Soil samples were taken from these sites as well as from existing well-studied agricultural and forest sites used as historical references by the National Science Foundation Long-Term Ecological Research Baltimore Ecosystem Study program. We found that the microbiomes in lawns of agricultural origin were similar to those in agricultural reference sites, which suggests that the ecological parameters on lawns and reference agricultural systems are similar in how they influence soil microbial community dynamics. In contrast, lawns that were previously forest showed distinct shifts in soil bacterial composition upon recent conversion but reverted back in composition similar to forest soils as the lawns aged over decades. Soil fungal communities shifted after forested land was converted to lawns, but unlike bacterial communities, did not revert in composition over time. Our results show that components of bacterial biodiversity and composition are resistant to change in previously forested lawns despite urbanization processes. Therefore land-use legacy, depending on the prior use, is an important factor to consider when examining urban ecological homogenization.

    

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