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1. Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation

   https://doi.org/10.1371/journal.pone.0245857  

   Wilson, R. M.; Zayed, A. A.; Crossen, K. B.; Woodcroft, B.; Tfaily, M. M.; Emerson, J.; Raab, N.; Hodgkins, S. B.; Verbeke, B.; Tyson, G.; et al (February 2021, PLOS ONE)

   Li, Huan (Ed.)

   Mechanisms controlling CO 2 and CH 4 production in wetlands are central to understanding carbon cycling and greenhouse gas exchange. However, the volatility of these respiration products complicates quantifying their rates of production in the field. Attempts to circumvent the challenges through closed system incubations, from which gases cannot escape, have been used to investigate bulk in situ geochemistry. Efforts towards mapping mechanistic linkages between geochemistry and microbiology have raised concern regarding sampling and incubation-induced perturbations. Microorganisms are impacted by oxygen exposure, increased temperatures and accumulation of metabolic products during handling, storage, and incubation. We probed the extent of these perturbations, and their influence on incubation results, using high-resolution geochemical and microbial gene-based community profiling of anaerobically incubated material from three wetland habitats across a permafrost peatland. We compared the original field samples to the material anaerobically incubated over 50 days. Bulk geochemistry and phylum-level microbiota in incubations largely reflected field observations, but divergence between field and incubations occurred in both geochemistry and lineage-level microbial composition when examined at closer resolution. Despite the changes in representative lineages over time, inferred metabolic function with regards to carbon cycling largely reproduced field results suggesting functional consistency. Habitat differences among the source materials remained the largest driver of variation in geochemical and microbial differences among the samples in both incubations and field results. While incubations may have limited usefulness for identifying specific mechanisms, they remain a viable tool for probing bulk-scale questions related to anaerobic C cycling, including CO 2 and CH 4 dynamics. 

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2. Lake Sediment Methane Responses to Organic Matter are Related to Microbial Community Composition in Experimental Microcosms

   https://doi.org/10.3389/fenvs.2022.834829  

   Bertolet, Brittni L.; Koepfli, Cristian; Jones, Stuart E. (March 2022, Frontiers in Environmental Science)

   Lake sediment microbial communities mediate carbon diagenesis. However, microbial community composition is variable across lakes, and it is still uncertain how variation in community composition influences sediment responses to environmental change. Sediment methane (CH 4 ) production has been shown to be substantially elevated by increased lake primary productivity and organic matter supply. However, the magnitude of the response of CH 4 production varies across lakes, and recent studies suggest a role for the microbial community in mediating this response. Here, we conducted sediment incubation experiments across 22 lakes to determine whether variation in sediment microbial community composition is related to the response of sediment CH 4 production to increases in organic matter. We sampled the 22 lakes across a gradient of pH in order to investigate lakes with variable sediment microbial communities. We manipulated the incubations with additions of dried algal biomass and show that variation in the response of CH 4 production to changes in organic matter supply is significantly correlated with metrics of sediment microbial community composition. Specifically, the diversity and richness of the non-methanogen community was most predictive of sediment CH 4 responses to organic matter additions. Additionally, neither metrics of microbial abundance nor preexisting organic matter availability explained meaningful variation in the response. Thus, our results provide experimental support that differences in sediment microbial communities influences CH 4 production responses to changes in organic matter availability. 

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3. Lignin, litter, and soil carbon decomposition from soil samples collected from 20 National Ecological Observatory Network (NEON) sites in 2019

   https://doi.org/10.6073/pasta/4d3e5a6df9c1fc4cea8d0be55a385182  

   Huang, Wenjuan; Yu, Wenjuan; Yi, Bo; Raman, Erik; Yang, Jihoon; Hammel, Kenneth E; Lu, Chaoqun; Howe, Adina Chuang; Weintraub-Leff, Samantha R; Hall, Steven J (January 2022, Environmental Data Initiative)

   We used incubations of soil and stable isotope measurements to measure lignin, litter, and SOC decomposition over an 18-month lab incubation and assessed their relationships with geochemical, microbial, N-related and climatic factors across 156 mineral soils collected from 20 National Ecological Observatory Network (NEON) sites, which span broad biophysical gradients (climate, soil, and vegetation type) across North America. The soils were collected in 2019. Lignin decomposition and biogeochemical variables were also measured in an approximately 12-month field incubation. 

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4. C Concentrations and Characterization Data from DOM Incubation Assay Experiments

   https://doi.org/10.6073/pasta/e1f848ac2a79d7caca8531d41fe7aef6  

   Kelly, Michelle Catherine; Bigcraft, Isaac; Kokate, Prajakta Paresh; Brown, Laura E; Kane, Evan; Techtmann, Stephen; Marcarelli, Amy (January 2025, Environmental Data Initiative)

   This dataset includes (1) original data from a dissolved organic carbon (DOC) incubation experiment and (2) a data synthesis of the DOC incubation experiment literature. Study component (1) was a factorial lab experiment crossing varying dissolved organic matter (DOM) sources (Suwannee River Fulvic Acid, Elliott soil leachate, Chlorella leachate) with varying microbial communities. The objective of this study component was to test the interacting effects of microbial community composition and DOM characteristics on carbon (C) biodegradation. We used a Micro-Oxymax Respirometer (Columbus Instruments, Columbus, Ohio) to measure carbon dioxide and oxygen accumulation at two hour intervals for a period of two weeks, and quantified the initial and final concentrations of dissolved organic carbon and total dissolved nitrogen of each experimental unit. To verify that the three DOM source solutions had differing chemical compositions and potential bioreactivity, we optically characterized each DOM source using mass spectra analysis and excitation-emission matrices (EEMs). Study component (2) is a synthesis of DOC concentrations from the C degradation experiment literature. The criteria for including a study in this synthesis was that (a) incubation DOM was sourced from a river, lake, marine, estuary, or marsh, and (b) that C concentrations were measured at least twice throughout the incubation in addition to an initial measurement. For each study, we extracted initial DOC values, elapsed incubation time, and reported DOC concentrations during the incubation period for each experimental treatment. This data package is completed. 

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5. Perspective: Simple State Communities to Study Microbial Interactions: Examples and Future Directions

   https://doi.org/10.3389/fmicb.2022.801864  

   Sarkar, Soumyadev; Ward, Kaitlyn; Kamke, Abigail; Ran, Qinghong; Feehan, Brandi; Richie, Tanner; Reese, Nicholas; Lee, Sonny T. (January 2022, Frontiers in Microbiology)

   Microbial interactions in natural environments are intricately complex. High numbers and rich diversity of microorganisms, along with compositional heterogeneities complicate the cause. It is essential to simplify these complex communities to understand the microbial interactions. We proposed a concept of “ simple state community ,” which represents a subset of microbes and/or microbial functions of the original population that is necessary to build a stable community. By combining microbial culturing and high-throughput sequencing, we can better understand microbe-microbe and microbe-host interactions. To support our proposed model, we used carbon-based and nitrogen-based media to capture the simple state communities. We used 16S rRNA amplicon sequencing and assigned taxonomic identity to the bacterial populations before and after simple state communities. We showed that simple state communities were a subset of the original microbial communities at both phyla and genera level. We further used shotgun metagenomics to gain insights into the functional potential of the assembled simple state communities. Our proposed model supported the goal of simplifying the complex communities across diverse systems to provide opportunity to facilitate comprehension of both the structure and function of the subset communities. Further applications of the concept include the high-throughput screening of simple state communities using the BIOLOG ® system and continuous culturing (Chemostat). This concept has the potential to test diverse experimental hypotheses in simplified microbial communities, and further extend that knowledge to answer the overarching questions at a more holistic level. 

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