Phytoplankton-derived polysaccharides and microbial peptidoglycans are key nutrients for deep-sea microbes in the Mariana Trench

BACKGROUND

The deep sea represents the largest marine ecosystem, driving global-scale biogeochemical cycles. Microorganisms are the most abundant biological entities and play a vital role in the cycling of organic matter in such ecosystems. The primary food source for abyssal biota is the sedimentation of particulate organic polymers. However, our knowledge of the specific biopolymers available to deep-sea microbes remains largely incomplete. One crucial rate-limiting step in organic matter cycling is the depolymerization of particulate organic polymers facilitated by extracellular enzymes (EEs). Therefore, the investigation of active EEs and the microbes responsible for their production is a top priority to better understand the key nutrient sources for deep-sea microbes.

RESULTS

In this study, we conducted analyses of extracellular enzymatic activities (EEAs), metagenomics, and metatranscriptomics from seawater samples of 50-9305 m from the Mariana Trench. While a diverse array of microbial groups was identified throughout the water column, only a few exhibited high levels of transcriptional activities. Notably, microbial populations actively transcribing EE genes involved in biopolymer processing in the abyssopelagic (4700 m) and hadopelagic zones (9305 m) were primarily associated with the class Actinobacteria. These microbes actively transcribed genes coding for enzymes such as cutinase, laccase, and xyloglucanase which are capable of degrading phytoplankton polysaccharides as well as GH23 peptidoglycan lyases and M23 peptidases which have the capacity to break down peptidoglycan. Consequently, corresponding enzyme activities including glycosidases, esterase, and peptidases can be detected in the deep ocean. Furthermore, cell-specific EEAs increased at 9305 m compared to 4700 m, indicating extracellular enzymes play a more significant role in nutrient cycling in the deeper regions of the Mariana Trench.

CONCLUSIONS

Transcriptomic analyses have shed light on the predominant microbial population actively participating in organic matter cycling in the deep-sea environment of the Mariana Trench. The categories of active EEs suggest that the complex phytoplankton polysaccharides (e.g., cutin, lignin, and hemicellulose) and microbial peptidoglycans serve as the primary nutrient sources available to deep-sea microbes. The high cell-specific EEA observed in the hadal zone underscores the robust polymer-degrading capacities of hadal microbes even in the face of the challenging conditions they encounter in this extreme environment. These findings provide valuable new insights into the sources of nutrition, the key microbes, and the EEs crucial for biopolymer degradation in the deep seawater of the Mariana Trench. Video Abstract.

Ecological function and interaction of different bacterial groups during alginate processing in coastal seawater community

The degradation of high molecular weight organic matter (HMWOM) is a core process of oceanic carbon cycle, which is determined by the activity of microbial communities harboring hundreds of different species. Illustrating the active microbes and their interactions during HMWOM processing can provide key information for revealing the relationship between community composition and its ecological functions. In this study, the genomic and transcriptional responses of microbial communities to the availability of alginate, an abundant HMWOM in coastal ecosystem, were elucidated. The main degraders transcribing alginate lyase (Aly) genes came from genera Alteromonas, Psychrosphaera and Colwellia. Meanwhile, some strains, mainly from the Rhodobacteraceae family, did not transcribe Aly gene but could utilize monosaccharides to grow. The co-culture experiment showed that the activity of Aly-producing strain could promote the growth of Aly-non-producing strain when alginate was the sole carbon source. Interestingly, this interaction did not reduce the alginate degradation rate, possibly due to the easily degradable nature of alginate. This study can improve our understanding of the relationship between microbial community activity and alginate metabolism function as well as further manipulation of microbial community structure for alginate processing.

Biogeography of culturable marine bacteria from both poles reveals that 'everything is not everywhere' at the genomic level

Based on 16S rRNA gene analyses, the same bacterial operational taxonomic units (OTUs) are common to both the Arctic and Antarctic oceans, supporting the concept 'everything is everywhere'. However, whether the same OTUs from both poles have identical genomes, i.e. whether 'everything is still everywhere' at the genomic level has not yet been examined systematically. Here, we isolated, sequenced and compared the genomes of 45 culturable marine bacteria belonging to three genera of Salinibacterium, Psychrobacter and Pseudoalteromonas from both polar oceans. The bacterial strains with identical 16S rRNA genes were common to both poles in every genus, and four identical genomes were detected in the genus Salinibacterium from the Arctic region. However, no identical genomes were observed from opposite poles in this study. Our data, therefore, suggest that 'everything is not everywhere' at the genomic level. The divergence time between bacteria is hypothesized to exert a strong impact on the bacterial biogeography at the genomic level. The geographical isolation between poles was observed for recently diverged, highly similar genomes, but not for moderately similar genomes. This study thus improves our understanding of the factors affecting the genomic-level biogeography of marine microorganisms isolated from distant locations.

Degradation and Utilization of Alginate by Marine Pseudoalteromonas: a Review

Alginate, which is mainly produced by brown algae and decomposed by heterotrophic bacteria, is an important marine organic carbon source. The genus Pseudoalteromonas contains diverse forms of heterotrophic bacteria that are widely distributed in marine environments and are an important group in alginate degradation. In this review, the diversity of alginate-degrading Pseudoalteromonas is introduced, and the characteristics of Pseudoalteromonas alginate lyases, including their sequences, enzymatic properties, structures, and catalytic mechanisms, and the synergistic effect of Pseudoalteromonas alginate lyases on alginate degradation are introduced. The acquisition of the alginate degradation capacity and the alginate utilization pathways of Pseudoalteromonas are also introduced. This paper provides a comprehensive overview of alginate degradation by Pseudoalteromonas, which will contribute to the understanding of the degradation and recycling of marine algal polysaccharides driven by marine bacteria.

Comparison of Alginate Utilization Pathways in Culturable Bacteria Isolated From Arctic and Antarctic Marine Environments

Alginate, mainly derived from brown algae, is an important carbon source that can support the growth of marine microorganisms in the Arctic and Antarctic regions. However, there is a lack of systematic investigation and comparison of alginate utilization pathways in culturable bacteria from both polar regions. In this study, 88 strains were isolated from the Arctic and Antarctic regions, of which 60 strains could grow in the medium with alginate as the sole carbon source. These alginate-utilizing strains belong to 9 genera of the phyla Proteobacteria and Bacteroidetes. The genomes of 26 alginate-utilizing strains were sequenced and genomic analyses showed that they all contain the gene clusters related to alginate utilization. The alginate transport systems of Proteobacteria differ from those of Bacteroidetes and there may be unique transport systems among different genera of Proteobacteria. The biogeographic distribution pattern of alginate utilization genes was further investigated. The alginate utilization genes are found to cluster according to bacterial taxonomy rather than geographic location, indicating that the alginate utilization genes do not evolve independently in both polar regions. This study systematically illustrates the alginate utilization pathways in culturable bacteria from the Arctic and Antarctic regions, shedding light into the distribution and evolution of alginate utilization pathways in polar bacteria.

Pelagovum pacificum gen. nov., sp. nov., a novel member of the family Rhodobacteraceae isolated from surface seawater of the Mariana Trench

A Gram-stain-negative, aerobic, ovoid-rod-shaped bacterium, designated strain SM1903^T, was isolated from surface seawater of the Mariana Trench. The strain grew at 15-37 °C (optimum, 35 °C) and with 1-15 % (optimum, 4 %) NaCl. It hydrolysed aesculin but did not reduce nitrate to nitrite and hydrolyse Tween 80. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1903^T formed a separate lineage within the family Rhodobacteraceae, sharing the highest 16S rRNA gene sequence similarity with type strains of Pseudooceanicola antarcticus (95.7 %) and Roseisalinus antarcticus (95.7 %). In phylogenetic trees based on single-copy OCs and whole proteins sequences, strain SM1903^T fell within a sub-cluster encompassed by Oceanicola granulosus, Roseisalinus antarcticus and Histidinibacterium lentulum and formed a branch adjacent to Oceanicola granulosus. The major cellular fatty acids were summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c), C_16 : 0 and 11-methyl-C_18 : 1  ω7c. The polar lipids mainly comprised phosphatidylglycerol, phosphatidylcholine, one unidentified lipid, one unidentified aminolipid, and one unidentified glycolipid. The solo respiratory quinone was ubiquinone-10. The genomic DNA G+C content of strain SM1903^T was 66.0 mol%. Based on the results of phenotypic, chemotaxonomic, and phylogenetic characterization for strain SM1903^T, it is considered to represent a novel species of a novel genus in the family Rhodobacteraceae, for which the name Pelagovum pacificum gen. nov., sp. nov. is proposed. The type strain is SM1903^T (=MCCC 1K03608^T=KCTC 72046^T).

Shewanella polaris sp. nov., a psychrotolerant bacterium isolated from Arctic brown algae

A Gram-stain-negative, facultatively anaerobic, flagellated and rod-shaped bacterium, designated strain SM1901T, was isolated from a brown algal sample collected from Kings Bay, Svalbard, Arctic. Strain SM1901T grew at -4‒30 °C and with 0-7.0 % (w/v) NaCl. It reduced nitrate to nitrite and hydrolysed DNA and Tween 80. Results of phylogenetic analyses based on 16S rRNA gene sequences indicated that strain SM1901T was affiliated with the genus Shewanella, showing the highest sequence similarity to the type strain of Shewanella litoralis (97.5%), followed by those of Shewanella vesiculosa, Shewanella livingstonensis and Shewanella saliphila (97.3 % for all three). The major cellular fatty acids were summed feature 3 (C16 : 1 ω7с and/or C16 : 1 ω6с), C16 : 0, C18 : 0, iso-C15 : 0 and C17 : 1 ω8с and the major polar lipids were phosphatidylethanolamine and phosphatidylglycerol. The respiratory quinones were ubiquinones Q-7, Q-8, menaquinones MK-7(H) and MK-8. The genome of strain SM1901T was 4648537 nucleotides long and encoded a variety of cold adaptation related genes, providing clues for better understanding the ecological adaptation mechanisms of polar bacteria. The genomic DNA G+C content of strain SM1901T was 40.5 mol%. Based on the polyphasic evidence presented in this paper, strain SM1901T was considered to represent a novel species, constituting a novel psychrotolerant lineage out of the known SF clade encompassed by polar Shewanella species, within the genus Shewanella, for which the name Shewanella polaris sp. nov. is proposed. The type strain is SM1901T (=KCTC 72047T=MCCC 1K03585T).

Reconstruction of the Functional Ecosystem in the High Light, Low Temperature Union Glacier Region, Antarctica

Antarctica is covered by multiple larger glaciers with diverse extreme conditions. Microorganisms in Antarctic regions are primarily responsible for diverse biogeochemical processes. The identity and functionality of microorganisms from polar glaciers are defined. However, little is known about microbial communities from the high elevation glaciers. The Union Glacier, located in the inland of West Antarctica at 79°S, is a challenging environment for life to survive due to the high irradiance and low temperatures. Here, soil and rock samples were obtained from three high mountains (Rossman Cove, Charles Peak, and Elephant Head) adjacent to the Union Glacier. Using metagenomic analyses, the functional microbial ecosystem was analyzed through the reconstruction of carbon, nitrogen and sulfur metabolic pathways. A low biomass but diverse microbial community was found. Although archaea were detected, bacteria were dominant. Taxa responsible for carbon fixation were comprised of photoautotrophs (Cyanobacteria) and chemoautotrophs (mainly Alphaproteobacterial clades: Bradyrhizobium, Sphingopyxis, and Nitrobacter). The main nitrogen fixation taxa were Halothece (Cyanobacteria), Methyloversatilis, and Leptothrix (Betaproteobacteria). Diverse sulfide-oxidizing and sulfate-reducing bacteria, fermenters, denitrifying microbes, methanogens, and methane oxidizers were also found. Putative producers provide organic carbon and nitrogen for the growth of other heterotrophic microbes. In the biogeochemical pathways, assimilation and mineralization of organic compounds were the dominant processes. Besides, a range of metabolic pathways and genes related to high irradiance, low temperature and other stress adaptations were detected, which indicate that the microbial communities had adapted to and could survive in this harsh environment. These results provide a detailed perspective of the microbial functional ecology of the Union Glacier area and improve our understanding of linkages between microbial communities and biogeochemical cycling in high Antarctic ecosystems.

Extracellular Enzyme Activity and Its Implications for Organic Matter Cycling in Northern Chinese Marginal Seas

Extracellular enzymes, initiating the degradation of organic macromolecules, are important functional components of marine ecosystems. Measuring in situ seawater extracellular enzyme activity (EEA) can provide fundamental information for understanding the biogeochemical cycling of organic matter in the ocean. Here we investigate the patterns of EEA and the major factors affecting the seawater EEA of Chinese marginal seas. The geographic distribution of EEA along a latitudinal transect was examined and found to be associated with dissolved organic carbon. Compared with offshore waters, inshore waters had higher enzyme activity. All the tested substrates were hydrolyzed at different rates and phosphatase, β-glucosidase and protease contributed greatly to summed hydrolysis rates. For any particular enzyme activity, the contribution of dissolved to total EEA was strongly heterogenous between stations. Comparisons of hydrolysis rates of the polymers and their corresponding oligomers suggest that molecule size does not necessarily limit the turnover of marine organic matter. In addition, several typical enzyme-producing clades, such as Bacteroidetes, Planctomycetes, Chloroflexi, Roseobacter, Alteromonas, and Pseudoalteromonas, were detected in the in situ environments. These enzyme-producing clades may be responsible for the production of different enzymes. Overall, each enzyme was found to flexibly respond to environmental conditions and were linked to microbial community composition. It is likely that this activity will profoundly affect organic matter cycling in the Chinese marginal seas.

Complete genome sequence of Pseudoalteromonas espejiana DSM9414T, an amino-acid-requiring strain from seawater

Strain DSM9414, the type strain of Pseudoalteromonas espejiana, is a Gram-negative, and amino-acid-requiring stain isolated from seawater off the coast of Northern California. In this study, we report the complete genome sequence of Pseudoalteromonas espejiana DSM9414^T. The genome (4,500,451bp; 40.3% G+C) is composed of two circular chromosomes: chromosome I is 3,720,756bp with 40.4% G+C content and chromosome II is 779,695bp with 39.8% G+C content. Genomic analysis showed that chromosome I encodes a complete set of ABC transporters responsible for branched-chain amino acids, whose homologous proteins were not discovered in other Pseudoalteromonas genomes released. This result indicated the tight dependence of extracellular amino acids for strain DSM9414^T, which is consistent with its phenotype. The complete genome sequence of P. espejiana provides further genetic insights into the diversity of dependence on extracellular amino acids for Pseudoalteromonas species.