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Metaproteomic analysis of microbial community structure and function in the South China Sea

ABSTRACT: In the present study, we studied microbial composition and metabolic activity in the euphotic zone of the South China Sea. 8 samples were collected and subjected to metaproteomic analysis. Our results suggested that mixotrophic phototrophs-driven NDL carbon fixation along with phytoplankton-driven NRL carbon fixation determined primary production in the oligotrophic ocean’s euphotic zone.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Phytoplankton Environmental Sample

SUBMITTER: keqiang yan

LAB HEAD: Dazhi Wang

PROVIDER: PXD018513 | Pride | 2024-06-16

REPOSITORIES: Pride

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	P1800820001_F10_1.raw	Raw
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	P1800820001_F2_1.raw	Raw

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Publications

Functional vertical connectivity of microbial communities in the ocean.

Chen Shi S Xie Zhang-Xian ZX Yan Ke-Qiang KQ Chen Jian-Wei JW Li Dong-Xu DX Wu Peng-Fei PF Peng Ling L Lin Lin L Dong Chun-Ming CM Zhao Zihao Z Fan Guang-Yi GY Liu Si-Qi SQ Herndl Gerhard J GJ Wang Da-Zhi DZ

Science advances 20240523 21

Sinking particles are a critical conduit for the transport of surface microbes to the ocean's interior. Vertical connectivity of phylogenetic composition has been shown; however, the functional vertical connectivity of microbial communities has not yet been explored in detail. We investigated protein and taxa profiles of both free-living and particle-attached microbial communities from the surface to 3000 m depth using a combined metaproteomic and 16<i>S</i> rRNA amplicon sequencing approach. A ...[more]

PMID: 38781332

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Illuminating the metabolic activities of deep-sea microbes and their functional adaptation to the harsh nutritional conditions with metaproteomics

Project description:In the present study, we studied microbial composition and metabolic activity in the bathypelagic zone of the South China Sea. 12 samples were collected and subjected to metaproteomic analysis. Our data provide a novel view of the roles of two lifestyle prokaryotes and their link in substrate utilization in dark ocean.

2024-06-16 | PXD026838 | Pride

In-depth metaproteome reveals carbon and nitrogen metabolic coupling throughout the water column in the South China Sea using 1-L seawater per sample

Project description:Marine microbes drive pivotal transformations in planetary-scale elemental cycles and have crucial impacts on global biogeochemical processes. Metaproteomics is a powerful tool for assessing the metabolic diversity and function of marine microbes. However, hundreds of liters of seawater are required for metaproteomic analysis due to the sparsity of microbial populations in seawater, which poses a substantial challenge to the widespread application of marine metaproteomics, particularly for deep seawater. Herein, a sensitive marine metaproteomics workflow, named SMMP, was developed by integrating polycarbonate filter-assisted microbial enrichment, solid-phase alkylation-based anti-interference metaproteome sample preparation and nanoLC-MS/MS for trace peptide separation and characterization. The method provided more than 8500 proteins from 1 L of bathypelagic seawater samples, which covered diverse microorganisms and crucial functions, e.g. the detection of key enzymes associated with the Wood-Ljungdahl pathway. Then, we applied SMMP to investigate vertical variations in the metabolic expression patterns of marine microorganisms from the euphotic zone to the bathypelagic zone. Methane oxidation and carbon monoxide (CO) oxidation were active processes, especially in the bathypelagic zone, as they provided a remarkable energy supply for the growth and proliferation of heterotrophic microorganisms. In addition, marker protein profiles detected related to ammonia transport, ammonia oxidation, and carbon fixation highlighted that Thaumarchaeota played a critical role in primary production based on the coupled carbon-nitrogen process, contributing to the storage of carbon and nitrogen in the bathypelagic regions. SMMP has low microbial input requirements and yields in-depth metaproteome analysis, making it a prospective approach for comprehensive marine metaproteomic investigations.

2024-04-16 | PXD051466 |

Response of Prochlorococcus to varying CO2:O2 ratios

Project description:Carbon fixation plays a central role in determining cellular redox poise, increasingly understood to be a key parameter in cyanobacterial physiology. In the cyanobacterium Prochlorococcus--—the most abundant phototroph in the oligotrophic oceans--—the carbon-concentrating mechanism (CCM) is reduced to the bare essentials. Given the ability of Prochlorococcus populations to grow under a wide range of oxygen concentrations in the ocean, we wondered how carbon and oxygen physiology intersect in this minimal phototroph. We monitored genome-wide transcription in cells shocked with acute limitation of CO2, O2, or both. O2 limitation produced much smaller transcriptional changes than the broad suppression seen under CO2 limitation and CO2/O2 co-limitation. Strikingly, the transcriptional responses evoked by both CO2 limitation conditions were initially similar to that previously seen in high light stress, but at later timepoints we observed O2-dependent recovery of photosynthesis-related transcripts. These results suggest that oxygen plays a protective role in Prochlorococcus when carbon fixation is not a sufficient sink for light energy.

2015-04-15 | GSE65684 | GEO

Response of Prochlorococcus to varying CO2:O2 ratios

2015-04-15 | E-GEOD-65684 | biostudies-arrayexpress

M. sedula transcriptional response under heterotrophic, autotrophic, and mixotrophic growth conditions

2009-11-01 | GSE14978 | GEO

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes

Project description:Although N2 fixation can occur in free-living cyanobacteria, the unicellular endosymbiotic cyanobacterium Candidatus Atelocyanobacterium thalassa (UCYN-A) is considered to be a dominant N2-fixing species in marine ecosystems. Four UCYN-A sublineages are known from partial nitrogenase (nifH) gene sequences. However, few studies have investigated their habitat preferences and regulation by their respective hosts in open-ocean versus coastal environments. Here, we compared UCYN-A transcriptomes from oligotrophic open-ocean versus nutrient-rich coastal waters. UCYN-A1 metabolism was more impacted by habitat changes than UCYN-A2. However, across habitats and sublineages genes for nitrogen fixation and energy production were highly transcribed. Curiously these genes, critical to the symbiosis for the exchange of fixed nitrogen for fixed carbon, maintained the same schedule of diel expression across habitats and UCYN-A sublineages, including UCYN-A3 in the open-ocean transcriptomes. Our results undersore the importance of nitrogen fixation in UCYN-A symbioses across habitats, with consequences for community interaction and global biogeochemical cycles.

2023-02-23 | GSE206403 | GEO

M. sedula transcriptional response under heterotrophic, autotrophic, and mixotrophic growth conditions

Project description:To study mixotrophy, it is desirable to have an organism capable of growth in the presence and absence of both organic and inorganic carbon sources, as well as organic and inorganic energy sources. Metallosphaera sedula is an extremely thermoacidophilic archaeon which has been shown to grow in the presence of inorganic carbon and energy source supplements (autotrophy), organic carbon and energy source supplements (heterotrophy), and in the presence of organic carbon and inorganic energy source supplements. The recent elucidation of M. sedulaâ??s inorganic carbon fixation cycle and its genome sequence further facilitate its use in mixotrophic studies. In this study, we grow M. sedula heterotrophically in the presence of organic carbon and energy sources (0.1% tryptone), autotrophically in the presence of inorganic carbon and energy sources (H2 + CO2), and â??mixotrophicallyâ?? in the presence of both organic and inorganic carbon and energy sources (0.1% tryptone + H2 + CO2 ) to characterize the nature of mixotrophy exhibited. Two 3 slide loops joined at equivalent conditions (8 slides total) for Mse cells includes 3 conditions tested in duplicate (biological repeats): heterotrophy (H1 and H2), autotrophy (A1 and A2), and mixotrophy (M1 and M2). Half of an RNA sample for one condition was labeled with Cy3 while the other half was labeled with Cy5. The two differently labeled samples were run on different slides. Each probe is spotted on each slide 5 times (5 replicates; spot intensities for all replicates on slide provided in associated raw data file).

2010-06-20 | E-GEOD-14978 | biostudies-arrayexpress

Anaerobic sulfur oxidation underlies adaptation of a chemosynthetic symbiont to oxic-anoxic interfaces

Project description:Chemosynthetic symbioses occur worldwide in marine habitats, but comprehensive physiological studies of chemoautotrophic bacteria thriving on animals are scarce. Stilbonematinae are coated by monocultures of thiotrophic Gammaproteobacteria. As these nematodes migrate through the redox zone, their ectosymbionts experience varying oxygen concentrations. Here, by applying omics, Raman microspectroscopy and stable isotope labeling, we investigated the effect of oxygen on the metabolism of Candidatus Thiosymbion oneisti. Unexpectedly, sulfur oxidation genes were upregulated in anoxic relative to oxic conditions, but carbon fixation genes and incorporation of 13C-labeled bicarbonate were not. Instead, several genes involved in carbon fixation, organic carbon assimilation and polyhydroxyalkanoate (PHA) biosynthesis, as well as nitrogen fixation and urea utilization were upregulated in oxic conditions. Furthermore, in the presence of oxygen, stress-related genes were upregulated together with vitamin biosynthesis genes likely necessary to withstand its deleterious effects, and fewer symbionts were detected to divide. Based on this first global physiological study of an uncultured chemosynthetic ectosymbiont, we propose that, in anoxic sediment, its proliferation is powered by anaerobic sulfur oxidation coupled to denitrification, whereas in upper layers it makes use of aerobic respiration to facilitate assimilation of carbon and nitrogen, and to survive oxidative stress. The ectosymbiont’s versatile metabolism is thus well-adapted to exploiting a highly changeable environment.

2020-04-30 | GSE146081 | GEO

Metaproteomics analysis of microbial structure on the surface of Indian Ocean

Project description:In this study we characterize microbial community features on the surface of Indian Ocean. 11 samples were collected from Indian Ocean and subjected for quantitative metaproteomics analysis for taxonomic and functional analysis. Our results suggested that metabolic tuning at metaproteomics levels enabled microbial community to sustain stable when subjected to environmental perturbations in the oligotrophic ocean.

2023-05-10 | PXD016285 | Pride

Co-expression analysis reveals distinct alliances around two carbon fixation pathways in hydrothermal vent symbionts

Project description:Biological carbon fixation is foundational to the biosphere. Most autotrophs are thought to possess one carbon fixation pathway. The hydrothermal vent tubeworm Riftia pachyptila’s chemoautotrophic symbionts, however, possess two functional pathways: the Calvin Benson-Bassham (CBB) and the reductive tricarboxylic acid (rTCA) cycles. Little is known about how Riftia’s symbionts and related organisms coordinate the functioning of these two pathways. Here we investigated net carbon fixation rates, transcriptional/metabolic responses, and transcriptional co-expression patterns of Riftia pachyptila’s endosymbionts by incubating tubeworms at environmental pressures, temperature, and geochemistry. Results showed that rTCA and CBB transcriptional patterns varied in response to different geochemical regimes and that each pathway is allied to specific metabolic processes, suggesting distinctive yet complementary roles in metabolic function. Net carbon fixation rates were also exemplary, and accordingly we propose that co-activity of CBB and rTCA may be an adaptation for maintaining high carbon fixation rates, conferring a fitness advantage in dynamic vent environments.

2024-03-28 | GSE249345 | GEO

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