skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


  • NSF Public Access
  • Search Results
  • Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation
Title: Functional capacities of microbial communities to carry out large scale geochemical processes are maintained during ex situ anaerobic incubation
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.  more » « less
Award ID(s):
2022070
PAR ID:
10291289
Author(s) / Creator(s):
; ; ; ; ; ; ; ; ; ; ; ; ;
Editor(s):
Li, Huan
Date Published:
Journal Name:
PLOS ONE
Volume:
16
Issue:
2
ISSN:
1932-6203
Page Range / eLocation ID:
e0245857
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; (, 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. 
    more » « less
  2. ; ; ; ; ; ; ; ; ; ; et al (, Environmental Research Letters)
    Abstract Quantifying the temperature sensitivity of methane (CH4) production is crucial for predicting how wetland ecosystems will respond to climate warming. Typically, the temperature sensitivity (often quantified as a Q10value) is derived from laboratory incubation studies and then used in biogeochemical models. However, studies report wide variation in incubation-inferred Q10values, with a large portion of this variation remaining unexplained. Here we applied observations in a thawing permafrost peatland (Stordalen Mire) and a well-tested process-rich model (ecosys) to interpret incubation observations and investigate controls on inferred CH4production temperature sensitivity. We developed a field-storage-incubation modeling approach to mimic the full incubation sequence, including field sampling at a particular time in the growing season, refrigerated storage, and laboratory incubation, followed by model evaluation. We found that CH4production rates during incubation are regulated by substrate availability and active microbial biomass of key microbial functional groups, which are affected by soil storage duration and temperature. Seasonal variation in substrate availability and active microbial biomass of key microbial functional groups led to strong time-of-sampling impacts on CH4production. CH4production is higher with less perturbation post-sampling, i.e. shorter storage duration and lower storage temperature. We found a wide range of inferred Q10values (1.2–3.5), which we attribute to incubation temperatures, incubation duration, storage duration, and sampling time. We also show that Q10values of CH4production are controlled by interacting biological, biochemical, and physical processes, which cause the inferred Q10values to differ substantially from those of the component processes. Terrestrial ecosystem models that use a constant Q10value to represent temperature responses may therefore predict biased soil carbon cycling under future climate scenarios. 
    more » « less
  3. ; ; ; ; ; ; ; (, Limnology and Oceanography: Methods)
    NA (Ed.)
    Abstract In vitro incubations using natural marine communities can provide insight into community structure and function in ways that are challenging through field observations alone. We have designed a minimal metal incubation system for controlled and repeatable experimentation of microbial communities. The systems, dubbed Pelagic Ecosystem Research Incubators (PERIcosms), are 115 L, conical tanks designed to sample suspended, settled, and wall associated material for month long periods. PERIcosms combine some of the ecological advantages of large volume mesocosm incubations with the experimental ease and replication of bottle incubations, and their design is accessible for use by researchers without specialized training or travel to a designated incubation facility. Here, we provide a detailed description for the construction and implementation of PERIcosms and demonstrate their potential to promote replicable, diverse communities for several weeks under clean conditions using time‐series results from two field experiments. One field experiment utilized coastal waters collected from Santa Catalina Island, CA and the other oligotrophic waters collected offshore of Honolulu, HI. Biomass metrics (chlorophyll a and particulate carbon) along with 16S/18S DNA based community composition assessments were conducted to show that communities contained within PERIcosms remained alive and diverse for several weeks using a semi‐continuous culturing approach. We detail trace metal clean techniques that can be used to minimize external contamination, particularly for low dissolved iron environments. PERIcosms have the potential to facilitate natural community incubations which are needed to continue advancing our understanding of microbial ecology and geochemistry. 
    more » « less
  4. ; ; ; ; ; ; ; ; ; ; et al (, The ISME Journal)
    Abstract In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients, and trace metals. However, the impacts of plume biogeochemistry on the oceans are poorly constrained due to a lack of integrated understanding of microbiomes, population genetics, and geochemistry. Here, we use microbial genomes to understand links between biogeography, evolution, and metabolic connectivity, and elucidate their impacts on biogeochemical cycling in the deep sea. Using data from 36 diverse plume samples from seven ocean basins, we show that sulfur metabolism defines the core microbiome of plumes and drives metabolic connectivity in the microbial community. Sulfur-dominated geochemistry influences energy landscapes and promotes microbial growth, while other energy sources influence local energy landscapes. We further demonstrated the consistency of links among geochemistry, function, and taxonomy. Amongst all microbial metabolisms, sulfur transformations had the highest MW-score, a measure of metabolic connectivity in microbial communities. Additionally, plume microbial populations have low diversity, short migration history, and gene-specific sweep patterns after migrating from background seawater. Selected functions include nutrient uptake, aerobic oxidation, sulfur oxidation for higher energy yields, and stress responses for adaptation. Our findings provide the ecological and evolutionary bases of change in sulfur-driven microbial communities and their population genetics in adaptation to changing geochemical gradients in the oceans. 
    more » « less
  5. ; ; ; ; ; (, Environmental Microbiology)
    Summary Marine microorganisms play a fundamental role in the global carbon cycle by mediating the sequestration of organic matter in ocean waters and sediments. A better understanding of how biological factors, such as microbial community composition, influence the lability and fate of organic matter is needed. Here, we explored the extent to which organic matter remineralization is influenced by species‐specific metabolic capabilities. We carried out aerobic time‐series incubations of Guaymas Basin sediments to quantify the dynamics of carbon utilization by two different heterotrophic marine isolates (Vibrio splendidus1A01;Pseudoalteromonassp. 3D05). Continuous measurement of respiratory CO2production and its carbon isotopic compositions (13C and14C) shows species‐specific differences in the rate, quantity and type of organic matter remineralized. Each species was incubated with hydrothermally‐influenced versus unimpacted sediments, resulting in a ~2‐fold difference in respiratory CO2yield across the experiments. Genomic analysis indicated that the observed carbon utilization patterns may be attributed in part to the number of gene copies encoding for extracellular hydrolytic enzymes. Our results demonstrate that the lability and remineralization of organic matter in marine environments is not only a function of chemical composition and/or environmental conditions, but also a function of the microorganisms that are present and active. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email