scholarly journals Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics

2017 ◽  
Vol 115 (3) ◽  
pp. E400-E408 ◽  
Author(s):  
Kristin Bergauer ◽  
Antonio Fernandez-Guerra ◽  
Juan A. L. Garcia ◽  
Richard R. Sprenger ◽  
Ramunas Stepanauskas ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Water Column ◽  
Compatible Solutes ◽  
Deep Ocean ◽  
Euphotic Zone ◽  
Atlantic Water ◽  
Phylogenetic Composition ◽  
Solute Transporters

The phylogenetic composition of the heterotrophic microbial community is depth stratified in the oceanic water column down to abyssopelagic layers. In the layers below the euphotic zone, it has been suggested that heterotrophic microbes rely largely on solubilized particulate organic matter as a carbon and energy source rather than on dissolved organic matter. To decipher whether changes in the phylogenetic composition with depth are reflected in changes in the bacterial and archaeal transporter proteins, we generated an extensive metaproteomic and metagenomic dataset of microbial communities collected from 100- to 5,000-m depth in the Atlantic Ocean. By identifying which compounds of the organic matter pool are absorbed, transported, and incorporated into microbial cells, intriguing insights into organic matter transformation in the deep ocean emerged. On average, solute transporters accounted for 23% of identified protein sequences in the lower euphotic and ∼39% in the bathypelagic layer, indicating the central role of heterotrophy in the dark ocean. In the bathypelagic layer, substrate affinities of expressed transporters suggest that, in addition to amino acids, peptides and carbohydrates, carboxylic acids and compatible solutes may be essential substrates for the microbial community. Key players with highest expression of solute transporters were Alphaproteobacteria, Gammaproteobacteria, and Deltaproteobacteria, accounting for 40%, 11%, and 10%, respectively, of relative protein abundances. The in situ expression of solute transporters indicates that the heterotrophic prokaryotic community is geared toward the utilization of similar organic compounds throughout the water column, with yet higher abundances of transporters targeting aromatic compounds in the bathypelagic realm.

scholarly journals Metaproteomics Reveals Similar Vertical Distribution of Microbial Transport Proteins in Particulate Organic Matter Throughout the Water Column in the Northwest Pacific Ocean

2021 ◽  
Vol 12 ◽  
Author(s):  
Ling-Fen Kong ◽  
Ke-Qiang Yan ◽  
Zhang-Xian Xie ◽  
Yan-Bin He ◽  
Lin Lin ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Communities ◽  
Water Column ◽  
Euphotic Zone ◽  
Transport Proteins ◽  
Energy Sources ◽  
Northwest Pacific ◽  
Twilight Zone ◽  
Northwest Pacific Ocean ◽  
The Northwest Pacific Ocean

Solubilized particulate organic matter (POM) rather than dissolved organic matter (DOM) has been speculated to be the major carbon and energy sources for heterotrophic prokaryotes in the ocean. However, the direct evidence is still lack. Here we characterized microbial transport proteins of POM collected from both euphotic (75 m, deep chlorophyll maximum DCM, and 100 m) and upper-twilight (200 m and 500 m) zones in three contrasting environments in the northwest Pacific Ocean using a metaproteomic approach. The proportion of transport proteins was relatively high at the bottom of the euphotic zone (200 m), indicating that this layer was the most active area of microbe-driven POM remineralization in the water column. In the upper-twilight zone, the predicted substrates of the identified transporters indicated that amino acids, carbohydrates, taurine, inorganic nutrients, urea, biopolymers, and cobalamin were essential substrates for the microbial community. SAR11, Rhodobacterales, Alteromonadales, and Enterobacteriales were the key contributors with the highest expression of transporters. Interestingly, both the taxonomy and function of the microbial communities varied among water layers and sites with different environments; however, the distribution of transporter types and their relevant organic substrates were similar among samples, suggesting that microbial communities took up similar compounds and were functionally redundant in organic matter utilization throughout the water column. The similar vertical distribution of transport proteins from the euphotic zone to the upper twilight zone among the contrasting environments indicated that solubilized POM rather than DOM was the preferable carbon and energy sources for the microbial communities.

scholarly journals Spatial organization of the kelp microbiome at micron scales

2020 ◽  
Author(s):  
S. Tabita Ramirez-Puebla ◽  
Brooke L. Weigel ◽  
Loretha Jack ◽  
Cathleen Schlundt ◽  
Catherine A. Pfister ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Water Column ◽  
Spatial Organization ◽  
Microbial Colonization ◽  
Dense Layer ◽  
Microbial Biofilm ◽  
Microbial Cells ◽  
Nereocystis Luetkeana ◽  
Spatially Differentiated

AbstractMacroalgae are colonized by complex and diverse microbial communities that are distinct from those on inert substrates, suggesting intimate symbioses that likely play key roles in both macroalgal and bacterial biology. Canopy-forming kelp fix teragrams of carbon per year in coastal kelp forest ecosystems, yet little is known about the structure and development of their associated microbial communities. We characterized the spatial organization of bacterial communities on blades of the canopy-forming kelp Nereocystis luetkeana using fluorescence in situ hybridization and spectral imaging with a probe set combining phylum, class and genus-level probes to target >90% of the microbial community. We show that kelp blades host a dense microbial biofilm, generally less than 20 μm thick, in which disparate microbial taxa live in close contact with one another. The biofilm is spatially differentiated, with tightly clustered cells of the dominant symbiont Granulosicoccus sp. (Gammaproteobacteria) close to the kelp surface and filamentous Bacteroidetes and Alphaproteobacteria relatively more abundant near the biofilm-seawater interface. Further, a community rich in Bacteroidetes colonized the interior of kelp tissues. Microbial community structure and cell density increased along the length of the kelp blade, from sparse microbial colonization of newly produced tissues at the meristematic base of the blade to an abundant microbial biofilm on older tissues at the blade tip. Finally, kelp from a declining population hosted fewer microbial cells compared to kelp from a stable population, indicating that biofilms are characteristic of health and that biofilm loss may be related to the condition of the host.ImportanceThe microbial community coating the surfaces of macroalgae may play a key but underexplored role both in the biology of the macroalgal host and in the biogeochemistry of the coastal ocean. We show that photosynthetic blades of the canopy-forming kelp Nereocystis luetkeana host a complex microbial biofilm that is both dense and spatially differentiated. Microbes of different taxa are in intimate cell-to-cell contact with one another; microbial cells invade the interior of kelp cells as well as cover their external surfaces; and a subset of the surface microbiota projects into the water column. These results highlight the potential for metabolic interactions between key members of the kelp microbiome as well as between microbes and their host. The dense layer of microbes coating the surface of the kelp blade is well-positioned to mediate interactions between the host and surrounding organisms and to modulate the chemistry of the surrounding water column.

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.

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>

scholarly journals Biogeophysical properties of an expansive Antarctic supraglacial stream

2016 ◽  
Vol 29 (1) ◽  
pp. 33-44 ◽  
Author(s):  
Michael D. SanClements ◽  
Heidi J. Smith ◽  
Christine M. Foreman ◽  
Marco Tedesco ◽  
Yu-Ping Chin ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Solar Radiation ◽  
Microbial Communities ◽  
Stream Water ◽  
Microbial Community Composition ◽  
Dry Valleys ◽  
Summer Temperatures ◽  
Aeolian Sediment ◽  
Variable Quality

AbstractSupraglacial streams are important hydrologic features in glaciated environments as they are conduits for the transport of aeolian debris, meltwater, solutes and microbial communities. We characterized the basic geomorphology, hydrology and biogeochemistry of the Cotton Glacier supraglacial stream located in the McMurdo Dry Valleys of Antarctica. The distinctive geomorphology of the stream is driven by accumulated aeolian sediment from the Transantarctic Mountains, while solar radiation and summer temperatures govern melt in the system. The hydrologic functioning of the Cotton Glacier stream is largely controlled by the formation of ice dams that lead to vastly different annual flow regimes and extreme flushing events. Stream water is chemically dilute and lacks a detectable humic signature. However, the fluorescent signature of dissolved organic matter (DOM) in the stream does demonstrate an extremely transitory red-shifted signal found only in near-stream sediment leachates and during the initial flushing of the system at the onset of flow. This suggests that episodic physical flushing drives pulses of DOM with variable quality in this stream. This is the first description of a large Antarctic supraglacial stream and our results provide evidence that the hydrology and geomorphology of supraglacial streams drive resident microbial community composition and biogeochemical cycling.

A method for measuring the response of sediment microbial communities to environmental perturbations

1984 ◽  
Vol 30 (11) ◽  
pp. 1408-1414 ◽  
Author(s):  
Akira Furutani ◽  
John W. M. Rudd ◽  
C. A. Kelly
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Microbial Communities ◽  
Nitrate Reduction ◽  
Microbial Processes ◽  
Mercury Methylation ◽  
Community Activity ◽  
Environmental Perturbations ◽  
Comprehensive Information

A method has been developed for studying direct and indirect responses of microbial processes in lake sediments to environmental perturbations. Responses of the entire microbial community as well as specific members of the community were studied using in vitro sediment systems for periods of weeks or months under control and experimentally perturbed conditions. Effects of perturbations at the community level were determined by comparing rates of organic matter decomposition (CO2 + CH4 production) in the control and test (acidified) systems. At the same time and under the same conditions, rates of specific processes such as mercury methylation and sulfate and nitrate reduction were assayed to see if these processes responded in the same manner as did the activity of the entire community. Acidification (lowering from pH 6.3 to 4.2) did not affect either community activity or nitrate reduction. However, decreases were observed in sulfate reduction and mercury methylation which were independent of community activity, suggesting that acidification may affect these two specific processes directly. Use of this method provides comprehensive information about the interaction of sediment microbial processes as they respond to environmental perturbations.

Temporal and Vertical Variation in Microbial Community Composition in Response to Physicochemical Characteristics in a Water Column of Highly Eutrophied Jinhae Bay, South Korea

2018 ◽  
Vol 28 (2) ◽  
pp. 65-77 ◽  
Author(s):  
Jiyoung Lee ◽  
Jae-Hyun Lim ◽  
Junhyung Park ◽  
Il-Nam Kim
Keyword(s):  
Microbial Community ◽  
South Korea ◽  
Microbial Communities ◽  
Water Column ◽  
Community Composition ◽  
Microbial Community Composition ◽  
Temporal Changes ◽  
Rrna Gene ◽  
Vertical Variation ◽  
Jinhae Bay

Microbial communities play an essential role in marine biogeochemical cycles. Physical and biogeochemical changes in Jinhae Bay, the most anthropogenically eutrophied bay on the coasts of South Korea, are well described, but less is known about the associated changes in microbial communities. Temporal and vertical variation in microbial communities at three depths (surface, middle, and bottom) at seven time points (June to December) at the J1 sampling site were investigated on the MiSeq platform based on the 16S rRNA gene. Overall, the microbial community was dominated by Proteobacteria, Cyanobacteria, and Bacteroidetes from June to November, whereas Firmicutes were dominant in December, especially in the middle and bottom layers. The results indicate that the microbial community composition strongly varied with temporal changes in the physicochemical water properties. Moreover, the community composition differed markedly between the surface and middle layers and the bottom layer in the summer, when the water column was strongly stratified and bottom water hypoxia developed. A redundancy analysis suggested a significant correlation between physicochemical variables (i.e., temperature, salinity, and oxygen concentration) and microbial community composition. This study indicates that temporal changes in water conditions and eutrophication-induced hypoxia effectively shape the structure of the microbial community.

scholarly journals Distribution of Archaeal and Bacterial communities in a subtropical reservoir

2015 ◽  
Vol 27 (4) ◽  
pp. 411-420 ◽  
Author(s):  
Laís Américo Soares ◽  
André Cordeiro Alves Dos Santos ◽  
Iolanda Cristina Silveira Duarte ◽  
Emiliana Manesco Romagnoli ◽  
Maria do Carmo Calijuri
Keyword(s):  
Organic Matter ◽  
Nutrient Cycling ◽  
Microbial Communities ◽  
Water Column ◽  
Bacterial Communities ◽  
Aquatic Ecosystems ◽  
Metabolic Plasticity ◽  
Environmental Process ◽  
Ecological Importance ◽  
The Relationship

Abstract Aim: Microbial communities play a central role in environmental process such as organic matter mineralization and the nutrient cycling process in aquatic ecosystems. Despite their ecological importance, variability of the structure of archaeal and bacterial communities in freshwater remains understudied. Methods In the present study we investigated the richness and density of archaea and bacteria in the water column and sediments of the Itupararanga Reservoir. We also evaluated the relationship between the communities and the biotic and abiotic characteristics. Samples were taken at five depths in the water column next to the dam and three depths next to the reservoir entrance. Results PCR-DGGE evaluation of the archaeal and bacterial communities showed that both were present in the water column, even in oxygenated conditions. Conclusions The density of the bacteria (qPCR) was greater than that of the archaea, a result of the higher metabolic plasticity of bacteria compared with archaea.

scholarly journals Illuminating microbial metabolic activities in the dark deep ocean with metaproteomics

2018 ◽  
Author(s):  
Zhang-Xian Xie ◽  
Shu-Feng Zhang ◽  
Hao Zhang ◽  
Ling-Fen Kong ◽  
Lin Lin ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Dissolved Organic Matter ◽  
Metabolic Activity ◽  
Deep Ocean ◽  
Viral Proteins ◽  
Life Forms ◽  
Cytoplasmic Proteins ◽  
Proteomic Study ◽  
Metabolic Activities

AbstractThe deep ocean is the largest habitat on earth and holds diverse microbial life forms. Significant advances have been made in microbial diversity and their genomic potential in the deep ocean, however, little is known about microbial metabolic activity that is crucial to regulate the bathypelagic carbon sequestration. Here, we characterized proteomes covering large particulate (>0.7 μm), small particulate (0.2-0.7 μm) and dissolved (10 kDa-0.2 μm) fractions collected at a depth of 3000 m in the South China Sea. The Rhodospirillales, SAR324, SAR11, Nitrosinae/Tectomicrobia were the major contributors in the particulate fraction whereas Alteromonadales and viruses dominated the dissolved counterpart. Frequent detection of transcription or translation proteins in the particulate fractions indicated active metabolism of SAR324, Archaea, SAR11, and possible viable surface microbes, e.g. Prochlorococcus. Transporters for diverse substrates were the most abundant functional groups, and numerous spectra of formate dehydrogenases and glycine betaine transporters unveiled the importance of methylated compounds for the survival of deep-sea microbes. Notably, abundant non-viral proteins, especially transporters and cytoplasmic proteins, were detected in the dissolved fraction, indicating their potential roles in nutrient scavenging and the stress response. Our size-based proteomic study implied the holistic microbial activity mostly acting on the labile dissolved organic matter as well as the potential activities of surface microbes and dissolved non-viral proteins in the deep ocean.ImportanceThe deep ocean produces one third of the biological CO2 in the ocean. However, little is known about metabolic activity of the bathypelagic microbial community which is crucial for understanding the biogeochemical cycling of organic matter, especially the formation of bulk refractory dissolved organic matter (DOM), one of the largest reservoirs of reduced carbon on Earth. This study provided the protein evidence firstly including both particulate and dissolved fractions to comprehensively decipher the active microbes and metabolic processes involved in the DOM recycling in the deep ocean. Our data supported the hypothesis of the carbon and energy supply from the labile DOM after the solution of sinking particles to the bathypelagic microbial community.

scholarly journals Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland

PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0260933
Author(s):  
Rachel L. Rubin ◽  
Kate A. Ballantine ◽  
Arden Hegberg ◽  
Jason P. Andras
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Soil Organic Matter ◽  
Microbial Communities ◽  
Ecological Restoration ◽  
Cation Exchange Capacity ◽  
Exchange Capacity ◽  
Soil Functions ◽  
Wetland Development ◽  
Denitrification Potential

Microbial communities are early responders to wetland degradation, and instrumental players in the reversal of this degradation. However, our understanding of soil microbial community structure and function throughout wetland development remains incomplete. We conducted a survey across cranberry farms, young retired farms, old retired farms, flooded former farms, ecologically restored former farms, and natural reference wetlands with no history of cranberry farming. We investigated the relationship between the microbial community and soil characteristics that restoration intends to maximize, such as soil organic matter, cation exchange capacity and denitrification potential. Among the five treatments considered, flooded and restored sites had the highest prokaryote and microeukaryote community similarity to natural wetlands. In contrast, young retired sites had similar communities to farms, and old retired sites failed to develop wetland microbial communities or functions. Canonical analysis of principal coordinates revealed that soil variables, in particular potassium base saturation, sodium, and denitrification potential, explained 45% of the variation in prokaryote communities and 44% of the variation in microeukaryote communities, segregating soil samples into two clouds in ordination space: farm, old retired and young retired sites on one side and restored, flooded, and natural sites on the other. Heat trees revealed possible prokaryotic (Gemmatimonadetes) and microeukaryotic (Rhizaria) indicators of wetland development, along with a drop in the dominance of Nucletmycea in restored sites, a class that includes suspected mycorrhizal symbionts of the cranberry crop. Flooded sites showed the strongest evidence of wetland development, with triple the soil organic matter accumulation, double the cation exchange capacity, and seventy times the denitrification potential compared to farms. However, given that flooding does not promote any of the watershed or habitat benefits as ecological restoration, we suggest that flooding can be used to stimulate beneficial microbial communities and soil functions during the restoration waiting period, or when restoration is not an option.

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