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 Antarctic Bacteria, Sea Ice Ecosystem Dynamics, and Global Climate Change

2021 ◽  
Author(s):  
◽  
Andrew Robert Martin
Keyword(s):  
Climate Change ◽  
Organic Matter ◽  
Microbial Community ◽  
Dissolved Organic Matter ◽  
Southern Ocean ◽  
Sea Ice ◽  
Metabolic Activity ◽  
Bacterial Response ◽  
Pack Ice ◽  
Fast Ice

<p>Productivity in the Southern Ocean reflects both the spatial and temporal dynamics of the sea ice ecosystem, as well as the complex cycling of energy through the microbial community. Marine bacteria are thought to be integral to trophodynamics and the functioning of a microbial loop within the ice matrix, but there is no clear understanding of the distribution and diversity of bacteria or the importance of bacterial production. Understanding the bacterial response to environmental change in the sea ice ecosystem may provide an insight into the potential changes to the physical oceanography and ecology of the Southern Ocean. In this study, a multivariate statistical approach was used to compare the distribution and abundance of bacteria occurring in pack ice at the tongue of the Mertz Glacier (George V Coast, Antarctica) with bacteria from fast ice at Cape Hallett (Victoria Land coastline, Antarctica). Estimates of bacterial abundance were derived using both epifluorescence microscopy and flow cytometry and correlated with algal and chlorophyll a data. Significant differences in the vertical distribution of cells within the ice were observed between the Mertz Glacier and Cape Hallett, but no overall difference in cell abundance was found between the two locations with 7.6 ± 1.2 x 109 cells per m2 and 8.7 ± 1.6 x 109 cells per m2 respectively. Bacteria and algae were positively correlated in pack ice of the Mertz Glacier indicating a functional microbial loop, but no discernable relationship was exhibited in multiyear ice at Cape Hallett. These findings support the general consensus that the generation of bacterial biomass from algal-derived dissolved organic matter is highly variable across seasons and habitats. The tetrazolium salt 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) was used to investigate the bacterial response to experimentally induced changes in light and salinity in fast ice at Cape Hallett. Two distinct assemblages were examined; the brine channel assemblage near the surface of the ice and the interstitial or bottom assemblage. This study presents preliminary evidence that the metabolic activity of brine bacteria is influenced by light stimulus, most likely as a response to increased levels of algal-derived dissolved organic matter. No cells were deemed to be metabolically active when incubated in the dark, while on average thirty-eight percent of the cells incubated at 150 =mol photons m-2 s-1 were metabolically active. Additional results indicate that salt concentration is more significant than light irradiance in influencing the metabolic response of cells present in the interstitial region of the sea ice profile. When acclimated over a period of eight hours, cells exhibited a tolerance to changing saline concentrations, but after a further eight hours there is some evidence to suggest activity is reduced at either end of the saline regime. Bacterial metabolic activity in each assemblage is thus thought to reflect the fundamentally different light and saline environments within the sea ice. Metabolic probes such as CTC will prove useful in providing a mechanistic understanding of productivity and trophodynamics in the Antarctic coastal ecosystem, and may contribute to prognostic models for qualifying the resilience of the microbial community to climate change.</p>

scholarly journals Antarctic Bacteria, Sea Ice Ecosystem Dynamics, and Global Climate Change

2021 ◽  
Author(s):  
◽  
Andrew Robert Martin
Keyword(s):  
Climate Change ◽  
Organic Matter ◽  
Microbial Community ◽  
Dissolved Organic Matter ◽  
Southern Ocean ◽  
Sea Ice ◽  
Metabolic Activity ◽  
Bacterial Response ◽  
Pack Ice ◽  
Fast Ice

<p>Productivity in the Southern Ocean reflects both the spatial and temporal dynamics of the sea ice ecosystem, as well as the complex cycling of energy through the microbial community. Marine bacteria are thought to be integral to trophodynamics and the functioning of a microbial loop within the ice matrix, but there is no clear understanding of the distribution and diversity of bacteria or the importance of bacterial production. Understanding the bacterial response to environmental change in the sea ice ecosystem may provide an insight into the potential changes to the physical oceanography and ecology of the Southern Ocean. In this study, a multivariate statistical approach was used to compare the distribution and abundance of bacteria occurring in pack ice at the tongue of the Mertz Glacier (George V Coast, Antarctica) with bacteria from fast ice at Cape Hallett (Victoria Land coastline, Antarctica). Estimates of bacterial abundance were derived using both epifluorescence microscopy and flow cytometry and correlated with algal and chlorophyll a data. Significant differences in the vertical distribution of cells within the ice were observed between the Mertz Glacier and Cape Hallett, but no overall difference in cell abundance was found between the two locations with 7.6 ± 1.2 x 109 cells per m2 and 8.7 ± 1.6 x 109 cells per m2 respectively. Bacteria and algae were positively correlated in pack ice of the Mertz Glacier indicating a functional microbial loop, but no discernable relationship was exhibited in multiyear ice at Cape Hallett. These findings support the general consensus that the generation of bacterial biomass from algal-derived dissolved organic matter is highly variable across seasons and habitats. The tetrazolium salt 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) was used to investigate the bacterial response to experimentally induced changes in light and salinity in fast ice at Cape Hallett. Two distinct assemblages were examined; the brine channel assemblage near the surface of the ice and the interstitial or bottom assemblage. This study presents preliminary evidence that the metabolic activity of brine bacteria is influenced by light stimulus, most likely as a response to increased levels of algal-derived dissolved organic matter. No cells were deemed to be metabolically active when incubated in the dark, while on average thirty-eight percent of the cells incubated at 150 =mol photons m-2 s-1 were metabolically active. Additional results indicate that salt concentration is more significant than light irradiance in influencing the metabolic response of cells present in the interstitial region of the sea ice profile. When acclimated over a period of eight hours, cells exhibited a tolerance to changing saline concentrations, but after a further eight hours there is some evidence to suggest activity is reduced at either end of the saline regime. Bacterial metabolic activity in each assemblage is thus thought to reflect the fundamentally different light and saline environments within the sea ice. Metabolic probes such as CTC will prove useful in providing a mechanistic understanding of productivity and trophodynamics in the Antarctic coastal ecosystem, and may contribute to prognostic models for qualifying the resilience of the microbial community to climate change.</p>

scholarly journals Microbial Community Structure Affects Marine Dissolved Organic Matter Composition

2016 ◽  
Vol 3 ◽  
Author(s):  
Elizabeth B. Kujawinski ◽  
Krista Longnecker ◽  
Katie L. Barott ◽  
Ralf J. M. Weber ◽  
Melissa C. Kido Soule
Keyword(s):  
Organic Matter ◽  
Community Structure ◽  
Microbial Community ◽  
Dissolved Organic Matter ◽  
Microbial Community Structure ◽  
Organic Matter Composition

Efficient export of carbon to the deep ocean through dissolved organic matter

Nature ◽  
2005 ◽  
Vol 433 (7022) ◽  
pp. 142-145 ◽  
Author(s):  
Charles S. Hopkinson ◽  
Joseph J. Vallino
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Deep Ocean

scholarly journals Picocyanobacteria and deep-ocean fluorescent dissolved organic matter share similar optical properties

2017 ◽  
Vol 8 (1) ◽  
Author(s):  
Zhao Zhao ◽  
Michael Gonsior ◽  
Jenna Luek ◽  
Stephen Timko ◽  
Hope Ianiri ◽  
...  
Keyword(s):  
Organic Matter ◽  
Optical Properties ◽  
Dissolved Organic Matter ◽  
Deep Ocean ◽  
Fluorescent Dissolved Organic Matter

scholarly journals SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter

mBio ◽  
2017 ◽  
Vol 8 (2) ◽  
Author(s):  
Zachary Landry ◽  
Brandon K. Swan ◽  
Gerhard J. Herndl ◽  
Ramunas Stepanauskas ◽  
Stephen J. Giovannoni
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Complex Mixture ◽  
Deep Ocean ◽  
Oxidative Enzymes ◽  
Flavin Mononucleotide ◽  
Biological Oxidation ◽  
Refractory Compounds ◽  
Cyclic Alkanes ◽  
Oxygen Insertion

ABSTRACTDeep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist.IMPORTANCECarbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle.

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