Emergent properties of microbial communities drive accelerated biogeochemical cycling in disturbed temperate forests

Ecology ◽  
2021 ◽  
Author(s):  
Ernest D Osburn ◽  
Brian D Badgley ◽  
Brian D Strahm ◽  
Frank O Aylward ◽  
J E Barrett
Keyword(s):  
Microbial Communities ◽  
Temperate Forests ◽  
Biogeochemical Cycling ◽  
Emergent Properties

scholarly journals Soil microbial communities and elk foraging intensity: implications for soil biogeochemical cycling in the sagebrush steppe

2017 ◽  
Vol 20 (2) ◽  
pp. 202-211 ◽  
Author(s):  
Lauren C. Cline ◽  
Donald R. Zak ◽  
Rima A. Upchurch ◽  
Zachary B. Freedman ◽  
Anna R. Peschel
Keyword(s):  
Microbial Communities ◽  
Soil Microbial Communities ◽  
Biogeochemical Cycling ◽  
Sagebrush Steppe ◽  
Soil Microbial

Unlocking the power of lake multiproxy analyses by understanding subsurface biosphere processes

2021 ◽  
Author(s):  
Camille Thomas ◽  
Hendrik Vogel ◽  
Daniel Ariztegui
Keyword(s):  
Microbial Communities ◽  
Lake Sediments ◽  
Biogeochemical Cycling ◽  
Dead Sea ◽  
Extracellular Dna ◽  
Lake Ohrid ◽  
Subsurface Biosphere ◽  
The Dead ◽  
Lake Towuti ◽  
Paleoenvironmental Reconstructions

<p>Lake sediments bear valuable information allowing multidisciplinary research to address paleoclimatic and paleoenvironmental reconstructions at regional to global scales. Sedimentological, geochemical, paleontological and biological tools are commonly used to tackle these questions, which are generally driven by a set of intricated parameters. Among them, the importance of biogeochemical cycling is largely acknowledged in the lake (paleo-) water columns and has been at the heart of most paleolimnological studies. The way these signals are transferred to lake sediments has largely been studied. However, microbial communities - the principal actors in the biogeochemical cycling framework - keep being active in the sediment, and continue to influence the preservation and retention of organic and inorganic matter while buried. Gathered within the “early diagenesis” black box, these processes, once qualified, can help better interpret the proxies they may influence, and even constitute new ones. Within this work, we provide examples showing that the integration of studies of the subsurface biosphere within geo- and paleo-limnology investigations can help unlock or secure the potential of multiproxy analysis for reconstructing the paleoenvironments, paleoclimates and paleo-ecology of lake basins. The use of now well-developed OMICS methods, through the analysis of environmental and/or ancient DNA and lipids in particular has been coupled to mineralogical, isotopic and magnetic information in the Dead Sea (Levant) to demonstrate the differential preservation of mineralogic and sedimentologic signals along the last two glacial-interglacial cycles (Thomas et al., 2015, 2016; Ebert et al., 2018). Similar signals have been unlocked in Lake Towuti (Indonesia) and in Laguna Potrok Aike (Argentina) (Vuillemin et al., 2015, 2017). In Lake Ohrid (North Macedonia/Albania), environmental DNA has provided limited inputs on that perspective (Thomas et al., 2020), but has shown that ancient/fossil DNA could provide valuable information regarding the lake primary productivity and the status of its watershed land-cover. Integrating OMICS methods to tackle the identity and activity of the ancient and modern subsurface biosphere of lakes therefore holds an immense potential not only for microbiology investigations, but also for paleoclimatic and paleoenvironmental reconstructions.</p><p>Ebert et al. (2018) Overwriting of sedimentary magnetism by bacterially mediated mineral alteration. Geology <strong>46</strong>, 2–5.</p><p>Thomas et al. (2016) Microbial sedimentary imprint on the deep Dead Sea sediment. The Depositional Record 1–21.</p><p>Thomas et al. (2020) Weak influence of paleoenvironmental conditions on the subsurface biosphere of lake ohrid over the last 515 ka. Microorganisms <strong>8</strong>, 1–20.</p><p>Thomas et al. (2015) Impact of paleoclimate on the distribution of microbial communities in the subsurface sediment of the Dead Sea. Geobiology <strong>13</strong>, 546–561.</p><p>Vuillemin et al. (2015) Recording of climate and diagenesis through fossil pigments and sedimentary DNA at Laguna Potrok Aike, Argentina. Biogeosciences Discussions <strong>12</strong>, 18345–18388.</p><p>Vuillemin et al. (2017) Preservation and Significance of Extracellular DNA in Ferruginous Sediments from Lake Towuti , Indonesia. Frontiers in Microbiology <strong>8</strong>, 1–15.</p>

scholarly journals Metagenome assembled genomes of novel taxa from an acid mine drainage environment

2021 ◽  
Author(s):  
Christen L. Grettenberger ◽  
Trinity L. Hamilton
Keyword(s):  
Acid Mine Drainage ◽  
16S Rrna ◽  
16S Rrna Gene ◽  
Microbial Communities ◽  
Mine Drainage ◽  
Biogeochemical Cycling ◽  
Rrna Gene ◽  
Metabolic Potential ◽  
Carbon And Nitrogen ◽  
Acid Mine

Acid mine drainage (AMD) is a global problem in which iron sulfide minerals oxidize and generate acidic, metal-rich water. Bioremediation relies on understanding how microbial communities inhabiting an AMD site contribute to biogeochemical cycling. A number of studies have reported community composition in AMD sites from 16S rRNA gene amplicons but it remains difficult to link taxa to function, especially in the absence of closely related cultured species or those with published genomes. Unfortunately, there is a paucity of genomes and cultured taxa from AMD environments. Here, we report 29 novel metagenome assembled genomes from Cabin Branch, an AMD site in the Daniel Boone National Forest, KY, USA. The genomes span 11 bacterial phyla and one Archaea and include taxa that contribute to carbon, nitrogen, sulfur, and iron cycling. These data reveal overlooked taxa that contribute to carbon fixation in AMD sites as well as uncharacterized Fe(II)-oxidizing bacteria. These data provide additional context for 16S rRNA gene studies, add to our understanding of the taxa involved in biogeochemical cycling in AMD environments, and can inform bioremediation strategies. IMPORTANCE Bioremediating acid mine drainage requires understanding how microbial communities influence geochemical cycling of iron and sulfur and biologically important elements like carbon and nitrogen. Research in this area has provided an abundance of 16S rRNA gene amplicon data. However, linking these data to metabolisms is difficult because many AMD taxa are uncultured or lack published genomes. Here, we present metagenome assembled genomes from 29 novel AMD taxa and detail their metabolic potential. These data provide information on AMD taxa that could be important for bioremediation strategies including taxa that are involved in cycling iron, sulfur, carbon, and nitrogen.

scholarly journals Mapping metabolic activity at single cell resolution in intact volcanic fumarole sediment

2020 ◽  
Vol 367 (1) ◽  
Author(s):  
Jeffrey J Marlow ◽  
Isabella Colocci ◽  
Sean P Jungbluth ◽  
Nils Moritz Weber ◽  
Amy Gartman ◽  
...  
Keyword(s):  
Structure Function ◽  
Microbial Communities ◽  
Metabolic Activity ◽  
Point Sources ◽  
Emergent Properties ◽  
Spatial Relationships ◽  
Environmental Regime ◽  
Novel Approach ◽  
Stable Conditions ◽  
Metabolite Exchange

ABSTRACT Interactions among microorganisms and their mineralogical substrates govern the structure, function and emergent properties of microbial communities. These interactions are predicated on spatial relationships, which dictate metabolite exchange and access to key substrates. To quantitatively assess links between spatial relationships and metabolic activity, this study presents a novel approach to map all organisms, the metabolically active subset and associated mineral grains, all while maintaining spatial integrity of an environmental microbiome. We applied this method at an outgassing fumarole of Vanuatu's Marum Crater, one of the largest point sources of several environmentally relevant gaseous compounds, including H2O, CO2 and SO2. With increasing distance from the sediment-air surface and from mineral grain outer boundaries, organism abundance decreased but the proportion of metabolically active organisms often increased. These protected niches may provide more stable conditions that promote consistent metabolic activity of a streamlined community. Conversely, exterior surfaces accumulate more organisms that may cover a wider range of preferred conditions, implying that only a subset of the community will be active under any particular environmental regime. More broadly, the approach presented here allows investigators to see microbial communities ‘as they really are’ and explore determinants of metabolic activity across a range of microbiomes.

Evaluation of the enzymatic activity and diversity of soil microorganism in Andean temperate forests degradation gradient

2020 ◽  
Author(s):  
Alejandro Atenas ◽  
Felipe Aburto ◽  
Rodrigo Hasbun ◽  
Carolina Merino
Keyword(s):  
Enzymatic Activity ◽  
Microbial Communities ◽  
Temperate Forests ◽  
Soil Microbial Communities ◽  
Forest Degradation ◽  
Soil Microorganism ◽  
Degraded Forest ◽  
Total N ◽  
Nothofagus Obliqua ◽  
Degraded Condition

<p>Soil microorganism are an essential component of forest ecosystem. Microbes and plant release enzymes that catalyse reactions needed to decomposed soil organic matter and crucial to release nutrient in available forms. Therefore, soil enzymes are relevant indicators of microbial activity and nutrient cycling in forest ecosystems. Anthropic disturbances in natural forest, such as logging and exotic livestock, modify the structure and composition of forest thereby altering the structure and activities of soil microbial communities.</p><p>Here we determine the effect of these disturbances on the enzymatic activity (Dehydrogenase-DHA; Phosphatase Acid-AP; Ureasa-UA) and the microbial diversity using a forest degradation gradient of native temperate forest dominated by Nothofagus dombeyi, Nothofagus obliqua and Nothofagus alpina. In addition we quantify C:N:P nutrient reservoirs, stoichiometry and available pools. Preliminary results suggest a higher activity of the DHA enzyme in degraded forest dominated by N. obliqua. AP and UA showed no relationship with the phosphorus and total nitrogen reservoirs. Forest degradation modify microbial communities, C:N:P stoichiometry, total and available nutrient pools, where the biggest pool of total C and N was registered on low degraded condition and decrease as degradation condition increase from medium to high degraded forest (74.44%; 65.35%; 48.05% for total C and 3.71; 3.41; 3.24 for total N respectively). Inverse relation was registered for total P pool were the highest pool was registered on high degraded condition (14963ppm; 13092ppm and 11299ppm from high to low degraded condition). Degraded sites were dominated mainly by members of Gammaproteobacteria, Alfaproteobacteria, Acidobacteria and Bacteroidia. Chitinophagaceae and Burkholderiacea were not detected in degraded plots, which suggest that some of the specialised functions carried by this groups could be lost. With respect to fungi Ascomycota and Basidomicota Phylum dominated the soil profiles. A species of the genus Clonostachys (Bionectriaceae) was identified, an endophyte fungus that acts as a saprophyte, also known to be a parasite of other fungi and some nematodes.</p><p>This research contributes to a better understanding of the direct effects of anthropic disturbances on the biogeochemical functioning of temperate forests and their relationship to the activity and composition of microbial communities.</p><p>Acknowledgment: Proyecto Reforestación Enel – UdeC</p>

scholarly journals Seasonal controls on snow distribution and aerial ablation at the snow-patch and landscape scales, McMurdo Dry Valleys, Antarctica

2013 ◽  
Vol 7 (3) ◽  
pp. 917-931 ◽  
Author(s):  
J. W. Eveland ◽  
M. N. Gooseff ◽  
D. J. Lampkin ◽  
J. E. Barrett ◽  
C. D. Takacs-Vesbach
Keyword(s):  
Microbial Communities ◽  
Snow Cover ◽  
Temporal Dynamics ◽  
Multiple Scales ◽  
Biogeochemical Cycling ◽  
Mcmurdo Dry Valleys ◽  
Dry Valleys ◽  
Snow Covered Area ◽  
Covered Area ◽  
Patch Scale

Abstract. Accumulated snow in the McMurdo Dry Valleys, while limited, has great ecological significance to subnivian soil environments. Though sublimation dominates the ablation process in this region, measurable increases in soil moisture and insulation from temperature extremes provide more favorable conditions with respect to subnivian soil communities. While precipitation is not substantial, significant amounts of snow can accumulate, via wind transport, in topographic lees along the valley bottoms, forming thousands of discontinuous snow patches. These patches have the potential to act as significant sources of local meltwater, controlling biogeochemical cycling and the landscape distribution of microbial communities. Therefore, determining the spatial and temporal dynamics of snow at multiple scales is imperative to understanding the broader ecological role of snow in this region. High-resolution satellite imagery acquired during the 2009–2010 and 2010–2011 austral summers was used to quantify the distribution of snow across Taylor and Wright valleys. Extracted snow-covered area from the imagery was used as the basis for assessing inter-annual variability and seasonal controls on accumulation and ablation of snow at multiple scales. In addition to landscape analyses, fifteen 1 km2 plots (3 in each of 5 study regions) were selected to assess the prevalence of snow cover at finer spatial scales, referred to herein as the snow-patch scale. Results confirm that snow patches tend to form in the same locations each year with some minor deviations observed. At the snow-patch scale, neighboring patches often exhibit considerable differences in aerial ablation rates, and particular snow patches do not reflect trends for snow-covered area observed at the landscape scale. These differences are presumably related to microtopographic influences acting on individual snow patches, such as wind sheltering and differences in snow depth due to the underlying topography. This highlights the importance of both the landscape and snow-patch scales in assessing the effects of snow cover on biogeochemical cycling and microbial communities.

scholarly journals Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

2006 ◽  
Vol 361 (1475) ◽  
pp. 2009-2021 ◽  
Author(s):  
Martin F Polz ◽  
Dana E Hunt ◽  
Sarah P Preheim ◽  
Daniel M Weinreich
Keyword(s):  
Microbial Communities ◽  
Division Of Labour ◽  
Population Diversity ◽  
Nutrient Concentrations ◽  
Emergent Properties ◽  
Marine Microbes ◽  
Whole Genomes ◽  
Population Sizes ◽  
Underlying Mechanisms ◽  
Diverse Groups

Microbes in the ocean dominate biogeochemical processes and are far more diverse than anticipated. Thus, in order to understand the ocean system, we need to delineate microbial populations with predictable ecological functions. Recent observations suggest that ocean communities comprise diverse groups of bacteria organized into genotypic (and phenotypic) clusters of closely related organisms. Although such patterns are similar to metazoan communities, the underlying mechanisms for microbial communities may differ substantially. Indeed, the potential among ocean microbes for vast population sizes, extensive migration and both homologous and illegitimate genetic recombinations, which are uncoupled from reproduction, challenges classical population models primarily developed for sexually reproducing animals. We examine possible mechanisms leading to the formation of genotypic clusters and consider alternative population genetic models for differentiation at individual loci as well as gene content at the level of whole genomes. We further suggest that ocean bacteria follow at least two different adaptive strategies, which constrain rates and bounds of evolutionary processes: the ‘opportuni-troph’, exploiting spatially and temporally variable resources; and the passive oligotroph, efficiently using low nutrient concentrations. These ecological lifestyle differences may represent a fundamental divide with major consequences for growth and predation rates, genome evolution and population diversity, as emergent properties driving the division of labour within microbial communities.

scholarly journals METABOLIC: High-throughput Profiling of Microbial Genomes for Functional Traits, Biogeochemistry, and Community-scale Metabolic Networks

2020 ◽  
Author(s):  
Zhichao Zhou ◽  
Patricia Q Tran ◽  
Adam M Breister ◽  
Yang Liu ◽  
Kristopher Kieft ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Ecology ◽  
Single Cell ◽  
Metabolic Networks ◽  
Biogeochemical Cycling ◽  
Microbial Interactions ◽  
Microbial Genomes ◽  
Biogeochemical Models ◽  
Genome Scale

Abstract Background: Advances in microbiome science are being driven in large part due to our ability to study and infer microbial ecology from genomes reconstructed from mixed microbial communities using metagenomics and single-cell genomics. Such omics-based techniques allow us to read genomic blueprints of microorganisms, decipher their functional capacities and activities, and reconstruct their roles in biogeochemical processes. Currently available tools for analyses of genomic data can annotate and depict metabolic functions to some extent, however, no standardized approaches are currently available for the comprehensive characterization of metabolic predictions, metabolite exchanges, microbial interactions, and contributions to biogeochemical cycling. Results: We present METABOLIC (METabolic And BiogeOchemistry anaLyses In miCrobes), a scalable software to advance microbial ecology and biogeochemistry using genomes at the resolution of individual organisms and/or microbial communities. The genome-scale workflow includes annotation of microbial genomes, motif validation of biochemically validated conserved protein residues, identification of metabolism markers, metabolic pathway analyses, and calculation of contributions to individual biogeochemical transformations and cycles. The community-scale workflow supplements genome-scale analyses with determination of genome abundance in the community, potential microbial metabolic handoffs and metabolite exchange, and calculation of microbial community contributions to biogeochemical cycles. METABOLIC can take input genomes from isolates, metagenome-assembled genomes, or from single-cell genomes. Results are presented in the form of tables for metabolism and a variety of visualizations including biogeochemical cycling potential, representation of sequential metabolic transformations, and community-scale metabolic networks using a newly defined metric ‘MN-score’ (metabolic network score). METABOLIC takes ~3 hours with 40 CPU threads to process ~100 genomes and metagenomic reads within which the most compute-demanding part of hmmsearch takes ~45 mins, while it takes ~5 hours to complete hmmsearch for ~3600 genomes. Tests of accuracy, robustness, and consistency suggest METABOLIC provides better performance compared to other software and online servers. To highlight the utility and versatility of METABOLIC, we demonstrate its capabilities on diverse metagenomic datasets from the marine subsurface, terrestrial subsurface, meadow soil, deep sea, freshwater lakes, wastewater, and the human gut.Conclusion: METABOLIC enables consistent and reproducible study of microbial community ecology and biogeochemistry using a foundation of genome-informed microbial metabolism, and will advance the integration of uncultivated organisms into metabolic and biogeochemical models. METABOLIC is written in Perl and R and is freely available at https://github.com/AnantharamanLab/METABOLIC under GPLv3.

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