scholarly journals Metabolic profiling suggests two sources of organic matter shape microbial activity, but not community composition, in New Zealand fjords

2019 ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Federico Baltar ◽  
Sergio E. Morales
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Microbial Activity ◽  
Community Composition ◽  
Sediment Resuspension ◽  
Metabolic Diversity ◽  
New Production ◽  
Metabolic Potential ◽  
Microbial Carbon ◽  
And Function

AbstractFjords are semi-enclosed marine systems with unique physical conditions that influence microbial communities structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial phylogeny and metabolic potential in response to environmental conditions (e.g. depth). In the open ocean new production from photosynthesis supplies organic matter to deeper aphotic layers, sustaining microbial activity. We measured the metabolic diversity and activity of microbial communities in fjords to determine patterns in metabolic potential across and within fjords, and whether these patterns could be explained by community composition modifications. We demonstrated that metabolic potential and activity are shaped by similar parameters as total (prokaryotic and eukaryotic) microbial communities. However, we identified increases in metabolic diversity and potential (but not in community composition) at near bottom (aphotic) sites consistent with the influence of sediments in deeper waters. Thus, while composition and function of the microbial community in the upper water column was likely shaped by marine snow and sinking POM generated by new production, deeper sites were strongly influenced by sediment resuspension of benthic organic matter generated from this or other sources (terrestrial, chemoautotrophic, microbial carbon loop), uncoupling the community composition and function dynamics.

scholarly journals Changes in Microbial Community Phylogeny and Metabolic Activity Along the Water Column Uncouple at Near Sediment Aphotic Layers in Fjords

2021 ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Federico Baltar ◽  
Sergio E. Morales
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Water Column ◽  
Microbial Activity ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Leucine Incorporation ◽  
Metabolic Potential ◽  
Near Surface ◽  
Potential Activity

Abstract Fjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial phylogeny and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. We profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing) to link metabolic potential, activity, and community composition to known community drivers. Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter imput than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between phylogeny and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.

Composition of low molecular weight organic substances affect total soil microbial activity independently of community composition.

2020 ◽  
Author(s):  
Louis J.P. Dufour ◽  
Anke. M. Herrmann ◽  
Julie Leloup ◽  
Cédric Przybylski ◽  
Luc Abbadie ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Microbial Activity ◽  
Community Composition ◽  
Metabolic Pathways ◽  
Heat Dissipation ◽  
Energy Content ◽  
Microbial Community Composition ◽  
Total Heat

<p>It has recently been suggested that microbial-derived material is an important constituent of soil organic matter, and accumulation of organic matter in soil is related to microbial activity and the composition of the microbial communities present. However, microbial activity is generally intimately related to the properties of the carbon substrate (e.g. molecular diversity, energy content) available for decomposition. It is important, therefore, to understand in more detail what the drivers of microbial activity and their associated metabolic pathways are: the composition of the microbial communities or the properties of the available organic substrate.</p><p>Water extractable organic matter from 6 different grassland and forest soils were added cross-wise to samples of each of the soils. The total heat dissipation was measured by isothermal calorimetry during a 23 h incubation period. Heat dissipation is a measure of total metabolic activity in the soil. The total CO<sub>2</sub> emission was also determined, by gas chromatography-mass spectrometry. The elemental composition of low molecular weight organic substances (LMWOS) was obtained by Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry, which allowed us to calculate the Nominal Oxidation State of Carbon (NOSC) from each exact molecular mass detected. The NOSC is related to the energy content of the molecules. The microbial composition was determined by 16S rRNA gene sequencing. This experimental design allowed us to evaluate potential links between microbial community composition and their metabolic pathways when different LMWOS are undergoing decomposition.</p><p>First, we found that the total heat dissipated and CO<sub>2</sub> emitted were associated with differences in the composition of LMWOS, independent of microbial community composition in the soil. We observed that the median of the total CO<sub>2</sub> emission was positively correlated with the weighted sum of the NOSC of each detected LMWOS. These results emphasise that a supply in available substrate with lower energy density (i.e. higher NOSC) may result in an increase in decarboxylation processes. Furthermore, total heat dissipated but not CO<sub>2</sub> was positively correlated to the molecular richness of LMWOS. This indicates that substrate with a higher molecular richness include also other metabolic pathways where CO<sub>2</sub> is not a decomposition end-product. Finally, we observed three different dynamics of heat dissipation during the 23 h incubation period. These dynamics were related to the microbial communities, but were independent of the LMWOS composition. The dynamic of heat dissipation were summarised by a Q<sub>t50</sub> index, i.e. the time required to release half of the heat dissipated in 23 h. The Q<sub>t50</sub> index was significantly correlated to the relative abundance of different bacterial taxa. In conclusion, whilst the short-term dynamics of substrate use appear to be associated with microbial community composition, the overall activity is more closely related to the composition of the available substrate.</p>

scholarly journals Microbial Community Composition and Function in Permanently Cold Seawater and Sediments from an Arctic Fjord of Svalbard

2011 ◽  
Vol 77 (6) ◽  
pp. 2008-2018 ◽  
Author(s):  
A. Teske ◽  
A. Durbin ◽  
K. Ziervogel ◽  
C. Cox ◽  
C. Arnosti
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Rrna Gene ◽  
Hydrolysis Rates ◽  
Arctic Fjord ◽  
Seawater Samples ◽  
And Function ◽  
Algal Extracts

ABSTRACTHeterotrophic microbial communities in seawater and sediments metabolize much of the organic carbon produced in the ocean. Although carbon cycling and preservation depend critically on the capabilities of these microbial communities, their compositions and capabilities have seldom been examined simultaneously at the same site. To compare the abilities of seawater and sedimentary microbial communities to initiate organic matter degradation, we measured the extracellular enzymatic hydrolysis rates of 10 substrates (polysaccharides and algal extracts) in surface seawater and bottom water as well as in surface and anoxic sediments of an Arctic fjord. Patterns of enzyme activities differed between seawater and sediments, not just quantitatively, in accordance with higher cell numbers in sediments, but also in their more diversified enzyme spectrum. Sedimentary microbial communities hydrolyzed all of the fluorescently labeled polysaccharide and algal extracts, in most cases at higher rates in subsurface than surface sediments. In seawater, in contrast, only 5 of the 7 polysaccharides and 2 of the 3 algal extracts were hydrolyzed, and hydrolysis rates in surface and deepwater were virtually identical. To compare bacterial communities, 16S rRNA gene clone libraries were constructed from the same seawater and sediment samples; they diverged strongly in composition. Thus, the broader enzymatic capabilities of the sedimentary microbial communities may result from the compositional differences between seawater and sedimentary microbial communities, rather than from gene expression differences among compositionally similar communities. The greater number of phylum- and subphylum-level lineages and operational taxonomic units in sediments than in seawater samples may reflect the necessity of a wider range of enzymatic capabilities and strategies to access organic matter that has already been degraded during passage through the water column. When transformations of marine organic matter are considered, differences in community composition and their different abilities to access organic matter should be taken into account.

scholarly journals Changes in microbial community phylogeny and metabolic activity along the water column uncouple at near sediment aphotic layers in fjords

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sven P. Tobias-Hünefeldt ◽  
Stephen R. Wing ◽  
Federico Baltar ◽  
Sergio E. Morales
Keyword(s):  
Organic Matter ◽  
Community Structure ◽  
Microbial Community ◽  
Water Column ◽  
Microbial Activity ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Leucine Incorporation ◽  
Metabolic Potential ◽  
Near Surface

AbstractFjords are semi-enclosed marine systems with unique physical conditions that influence microbial community composition and structure. Pronounced organic matter and physical condition gradients within fjords provide a natural laboratory for the study of changes in microbial community structure and metabolic potential in response to environmental conditions. Photosynthetic production in euphotic zones sustains deeper aphotic microbial activity via organic matter sinking, augmented by large terrestrial inputs. Previous studies do not consider both prokaryotic and eukaryotic communities when linking metabolic potential and activity, community composition, and environmental gradients. To address this gap we profiled microbial functional potential (Biolog Ecoplates), bacterial abundance, heterotrophic production (3H-Leucine incorporation), and prokaryotic/eukaryotic community composition (16S and 18S rRNA amplicon gene sequencing). Similar factors shaped metabolic potential, activity and community (prokaryotic and eukaryotic) composition across surface/near surface sites. However, increased metabolic diversity at near bottom (aphotic) sites reflected an organic matter influence from sediments. Photosynthetically produced particulate organic matter shaped the upper water column community composition and metabolic potential. In contrast, microbial activity at deeper aphotic waters were strongly influenced by other organic matter input than sinking marine snow (e.g. sediment resuspension of benthic organic matter, remineralisation of terrestrially derived organic matter, etc.), severing the link between community structure and metabolic potential. Taken together, different organic matter sources shape microbial activity, but not community composition, in New Zealand fjords.

scholarly journals Metabolic Diversity within the Globally Abundant Marine Group IIEuryarchaeaOffers Insight into Ecological Patterns

2018 ◽  
Author(s):  
Benjamin J Tully
Keyword(s):  
Organic Matter ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Metabolic Diversity ◽  
Metabolic Potential ◽  
Surface Ocean ◽  
Ecological Patterns ◽  
Reference Genomes ◽  
Insight Into

AbstractDespite their discovery over 25 years ago, the Marine Group IIEuryarchaea(MGII) have remained a difficult group of organisms to study, lacking cultured isolates and genome references. The MGII have been identified in marine samples from around the world and evidence supports a photoheterotrophic lifestyle combining phototrophy via proteorhodopsins with the remineralization of high molecular weight organic matter. Divided between two clades, the MGII have distinct ecological patterns that are not understood based on the limited number of available genomes. Here, I present the comparative genomic analysis of 250 MGII genomes, providing the most detailed view of these mesophilic archaea to-date. This analysis identified 17 distinct subclades including nine subclades that previously lacked reference genomes. The metabolic potential and distribution of the MGII genera revealed distinct roles in the environment, identifying algal-saccharide-degrading coastal subclades, protein-degrading oligotrophic surface ocean subclades, and mesopelagic subclades lacking proteorhodopsins common in all other subclades. This study redefines the MGII and provides an avenue for understanding the role these organisms play in the cycling of organic matter throughout the water column.

scholarly journals Microbial communities across a hillslope-riparian transect shaped by proximity to the stream, groundwater table, and weathered bedrock

2018 ◽  
Author(s):  
Adi Lavy ◽  
David Geller McGrath ◽  
Paula B. Matheus Carnevali ◽  
Jiamin Wan ◽  
Wenming Dong ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Riparian Zone ◽  
Limited Information ◽  
Metabolic Potential ◽  
Carbon And Nitrogen ◽  
East River ◽  
Mountainous Watersheds ◽  
Geochemical Analyses ◽  
Selenium Reduction ◽  
And Function

AbstractWatersheds are important suppliers of freshwater for human societies. Within mountainous watersheds, microbial communities impact water chemistry and element fluxes as water from precipitation events discharges through soils and underlying weathered rock, yet there is limited information regarding the structure and function of these communities. Within the East River, CO watershed, we conducted a depth-resolved, hillslope to riparian zone transect study to identify factors that control how microorganisms are distributed and their functions. Metagenomic and geochemical analyses indicate that distance from the East River and proximity to groundwater and underlying weathered shale strongly impact microbial community structure and metabolic potential. Riparian zone microbial communities are compositionally distinct from all hillslope communities. Bacteria from phyla lacking isolated representatives consistently increase in abundance with increasing depth, but only in the riparian zone saturated sediments did we find Candidate Phyla Radiation bacteria. Riparian zone microbial communities are functionally differentiated from hillslope communities based on their capacities for carbon and nitrogen fixation and sulfate reduction. Selenium reduction is prominent at depth in weathered shale and saturated riparian zone sediments. We anticipate that the drivers of community composition and metabolic potential identified throughout the studied transect will predict patterns across the larger watershed hillslope system.

Dissimilar bacterial and fungal decomposer communities across rich to poor fen peatlands exhibit functional redundancy

2015 ◽  
Vol 95 (3) ◽  
pp. 219-230 ◽  
Author(s):  
Kristine M. Haynes ◽  
Michael D. Preston ◽  
James W. McLaughlin ◽  
Kara Webster ◽  
Nathan Basiliko
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Environmental Changes ◽  
Functional Redundancy ◽  
Organic Substrates ◽  
Metabolic Potential ◽  
Vegetation Communities ◽  
Chemical Complexity ◽  
Poor Fen

Haynes, K. M., Preston, M. D., McLaughlin, J. W., Webster, K. and Basiliko, N. 2015. Dissimilar bacterial and fungal decomposer communities across rich to poor fen peatlands exhibit functional redundancy. Can. J. Soil Sci. 95: 219–230. Climatic and environmental changes can lead to shifts in the dominant vegetation communities present in northern peatland ecosystems, including from Sphagnum- to vascular-dominated systems. Such shifts in vegetation result in changes to the chemical quality of carbon substrates for soil microbial decomposers, with leaves and roots deposited in the peat surface and subsurface that potentially decompose faster. This study characterized the bacterial and fungal communities present along a nutrient gradient ranging from rich to poor fen peatlands and assessed the metabolic potential of these communities to mineralize a variety of organic matter substrates of varying chemical complexity using substrate-induced respiration (SIR) assays. Distinct microbial communities existed between rich, intermediate and poor fens, but SIR in each of the three sites exhibited the same pattern of carbon mineralization, providing support for the concept of functional redundancy, at least under standardized in vitro conditions. Preferential mineralization of simple organic substrates in the rich fen and complex compounds in the poor fen was not observed. Similarly, no preference was given to “native” organic matter extracts derived from each fen, with microbial communities opting for the most bioavailable substrate. This study suggests that soil bacteria and fungi might be able to respond relatively rapidly to shifts in vegetation communities and subsequent changes in the quality of carbon substrate additions to peatlands associated with environmental and climatic change.

Permafrost-derived dissolved organic matter character controls microbial community composition in Arctic coastal waters

2021 ◽  
Author(s):  
Anders Dalhoff Bruhn ◽  
Colin A. Stedmon ◽  
Jérôme Comte ◽  
Atsushi Matsuoka ◽  
Neik Jesse Speetjens ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Community Composition ◽  
Relative Abundance ◽  
Microbial Community Composition ◽  
The Arctic ◽  
Glacial Deposit ◽  
Deposit Type ◽  
Lacustrine Deposit

<p>Climate warming is accelerating erosion rates along permafrost-dominated Arctic coasts. To study the impact of erosion on marine microbial community composition and growth in the Arctic coastal zone, dissolved organic matter (DOM) from three representative glacial landscapes (fluvial, lacustrine and moraine) along the Yukon coastal plain, are provided as substrate to marine bacteria using a chemostat setup. Our results indicate that chemostat cultures with a flushing rate of approximately a day provide comparable DOM bioavailability estimates to those from bottle experiments lasting weeks to months. DOM composition (inferred from UV-Visible spectroscopy) and biodegradability (inferred from DOC concentration, bacterial production and respiration) significantly differed between the three glacial deposit types. DOM from fluvial and moraine deposit types shows more terrestrial characteristics with lower aromaticity (S<sub>R</sub>: 0.63 (±0.02), SUVA<sub>254</sub>: 1.65 (±0.06) respectively S<sub>R</sub>: 0.68 (±0.00), SUVA<sub>254</sub>: 1.17 (±0.06)) compared to the lacustrine deposit type (S<sub>R</sub>: 0.71 (±0.02), SUVA<sub>254</sub>: 2.15 (±0.05)). The difference in composition of DOM corresponds with the development of three distinct microbial communities, with a dominance of Alphaproteobacteria for fluvial and lacustrine deposit types (relative abundance 0.67 and 0.87 respectively) and a dominance of Gammaproteobacteria for moraine deposit type (relative abundance 0.88). Bacterial growth efficiency (BGE) is 66% for moraine-derived DOM, while 13% and 28% for fluvial-derived and lacustrine-derived DOM respectively. The three microbial communities therefore differ in their net effect on DOM utilization. The higher BGE value for moraine-derived DOM was found to be due to a larger proportion of labile colourless DOM. The results from this study, therefore indicate a substrate control of marine microbial community composition and activities, suggesting that the effect of permafrost thaw and erosion in the Arctic coastal zone will depend on subtle differences in DOM related to glacial deposit types. These differences further determines the speed and extent of DOM mineralization and thereby carbon channelling into biomass in the microbial food web. We therefore conclude that marine microbes strongly respond to the input of terrestrial DOM released during coastal erosion of Arctic glacial landscapes.</p>

Investigating nutrient controls over microbial activity in tropical soils

2021 ◽  
Author(s):  
Lucia Fuchslueger
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Microbial Communities ◽  
Microbial Activity ◽  
Microbial Growth ◽  
Tropical Soils ◽  
Phosphorus Availability ◽  
Soil P ◽  
Soil Microbial ◽  
Low Phosphorus

<p>The Amazon rainforest is an important sink for atmospheric CO<sub>2</sub> counteracting increased emissions from anthropogenic fossil fuel combustion and land use change storing large amounts of carbon in plant biomass and soils. However, large parts of the Amazon Basin are characterized by highly weathered soils (ultisols and oxisols) with low availability of rock-derived phosphorus (and cations), which are mostly occluded in soil or bound in organic matter. Such low phosphorus availability is thought to be (co-)limiting plant productivity. However, much less is known whether low phosphorus availability influences the activity of heterotrophic microbial communities controlling litter and soil organic matter decomposition and thereby long-term carbon sequestration in tropical soils.</p><p>In tropical soils high temperature and humid conditions allow overall high microbial activity. Over a larger soil phosphorus fertility gradient across several Amazonian rainforest sites, at low P sites almost 40 % of total P was stored in microbial biomass, highlighting the competitive strength of microorganisms and their importance as P reservoir. Across all sites soil microbial biomass was a significant predictor for soil microbial respiration, but mass-specific respiration rates (normalized by microbial biomass C) rather decreased at higher soil P. Using the incorporation of <sup>18</sup>O from labelled water into DNA (i.e., a substrate-independent method) to determine microbial growth, we found significantly lower microbial growth rates per unit of microbial biomass at higher soil P. This resulted in a lower microbial carbon use efficiency, at a narrower C:P stoichiometry in soils with higher P levels, and pointed towards a microbial co-limitation of phosphorus and carbon at low soil P levels. Furthermore, data from a multi-year nutrient manipulation experiment in French Guiana and from short-term lab incubations suggest that microbial communities thriving at low P levels are highly efficient in taking up and storing added P, but do not necessarily respond with increased growth.</p><p>Soil microbial communities play a crucial role in soil carbon and phosphorus cycling in tropical soils as potent competitors for available P. They also play an important role in storing and buffering P losses from highly weathered tropical soils. The potential non-homoeostatic stoichiometric behavior of microbial communities in P cycling is important to consider in soil and ecosystem models based on stoichiometric relationships.</p>

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