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1.
Mol Ecol ; 33(12): e17385, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38738821

ABSTRACT

Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.


Subject(s)
Gene Transfer, Horizontal , Plants/microbiology , Plants/genetics , Microbiota/genetics , Phylogeny , Adaptation, Physiological/genetics , Genome, Bacterial/genetics , Ecosystem , Atlantic Ocean , Biological Evolution , Seawater/microbiology
2.
Microbiome ; 12(1): 77, 2024 Apr 25.
Article in English | MEDLINE | ID: mdl-38664737

ABSTRACT

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.


Subject(s)
Bacteria , Metagenomics , Nutrients , Peptidoglycan , Phytoplankton , Polysaccharides , Seawater , Polysaccharides/metabolism , Seawater/microbiology , Phytoplankton/metabolism , Phytoplankton/genetics , Nutrients/metabolism , Peptidoglycan/metabolism , Bacteria/classification , Bacteria/genetics , Bacteria/metabolism , Bacteria/isolation & purification , Microbiota
3.
Appl Environ Microbiol ; 90(2): e0202523, 2024 Feb 21.
Article in English | MEDLINE | ID: mdl-38259074

ABSTRACT

Marine bacteria play important roles in the degradation and cycling of algal polysaccharides. However, the dynamics of epiphytic bacterial communities and their roles in algal polysaccharide degradation during kelp decay are still unclear. Here, we performed metagenomic analyses to investigate the identities and predicted metabolic abilities of epiphytic bacterial communities during the early and late decay stages of the kelp Saccharina japonica. During kelp decay, the dominant epiphytic bacterial communities shifted from Gammaproteobacteria to Verrucomicrobia and Bacteroidetes. In the early decay stage of S. japonica, epiphytic bacteria primarily targeted kelp-derived labile alginate for degradation, among which the gammaproteobacterial Vibrionaceae (particularly Vibrio) and Psychromonadaceae (particularly Psychromonas), abundant in alginate lyases belonging to the polysaccharide lyase (PL) families PL6, PL7, and PL17, were key alginate degraders. More complex fucoidan was preferred to be degraded in the late decay stage of S. japonica by epiphytic bacteria, predominantly from Verrucomicrobia (particularly Lentimonas), Pirellulaceae of Planctomycetes (particularly Rhodopirellula), Pontiellaceae of Kiritimatiellota, and Flavobacteriaceae of Bacteroidetes, which depended on using glycoside hydrolases (GHs) from the GH29, GH95, and GH141 families and sulfatases from the S1_15, S1_16, S1_17, and S1_25 families to depolymerize fucoidan. The pathways for algal polysaccharide degradation in dominant epiphytic bacterial groups were reconstructed based on analyses of metagenome-assembled genomes. This study sheds light on the roles of different epiphytic bacteria in the degradation of brown algal polysaccharides.IMPORTANCEKelps are important primary producers in coastal marine ecosystems. Polysaccharides, as major components of brown algal biomass, constitute a large fraction of organic carbon in the ocean. However, knowledge of the identities and pathways of epiphytic bacteria involved in the degradation process of brown algal polysaccharides during kelp decay is still elusive. Here, based on metagenomic analyses, the succession of epiphytic bacterial communities and their metabolic potential were investigated during the early and late decay stages of Saccharina japonica. Our study revealed a transition in algal polysaccharide-degrading bacteria during kelp decay, shifting from alginate-degrading Gammaproteobacteria to fucoidan-degrading Verrucomicrobia, Planctomycetes, Kiritimatiellota, and Bacteroidetes. A model for the dynamic degradation of algal cell wall polysaccharides, a complex organic carbon, by epiphytic microbiota during kelp decay was proposed. This study deepens our understanding of the role of epiphytic bacteria in marine algal carbon cycling as well as pathogen control in algal culture.


Subject(s)
Edible Seaweeds , Flavobacteriaceae , Kelp , Laminaria , Microbiota , Phaeophyceae , Humans , Metagenome , Kelp/metabolism , Polysaccharides/metabolism , Alginates/metabolism , Flavobacteriaceae/genetics , Flavobacteriaceae/metabolism , Carbon/metabolism
4.
Appl Environ Microbiol ; 90(1): e0170423, 2024 01 24.
Article in English | MEDLINE | ID: mdl-38169280

ABSTRACT

Catabolism of algal polysaccharides by marine bacteria is a significant process of marine carbon cycling. ß1,3/1,4-Mixed-linkage xylan (MLX) is a class of xylan in the ocean, widely present in the cell walls of red algae. However, the catabolic mechanism of MLX by marine bacteria remains elusive. Recently, we found that a marine Bacteroidetes strain, Polaribacter sp. Q13, is a specialist in degrading MLX, which secretes a novel MLX-specific xylanase. Here, the catabolic specialization of strain Q13 to MLX was studied by multiomics and biochemical analyses. Strain Q13 catabolizes MLX with a canonical starch utilization system (Sus), which is encoded by a single xylan utilization locus, XUL-Q13. In this system, the cell surface glycan-binding protein SGBP-B captures MLX specifically, contributing to the catabolic specificity. The xylanolytic enzyme system of strain Q13 is unique, and the enzymatic cascade dedicates the stepwise hydrolysis of the ß1,3- and ß1,4-linkages in MLX in the extracellular, periplasmic, and cytoplasmic spaces. Bioinformatics analysis and growth observation suggest that other marine Bacteroidetes strains harboring homologous MLX utilization loci also preferentially utilize MLX. These results reveal the catabolic specialization of MLX degradation by marine Bacteroidetes, leading to a better understanding of the degradation and recycling of MLX driven by marine bacteria.IMPORTANCERed algae contribute substantially to the primary production in marine ecosystems. The catabolism of red algal polysaccharides by marine bacteria is important for marine carbon cycling. Mixed-linkage ß1,3/1,4-xylan (MLX, distinct from hetero-ß1,4-xylans from terrestrial plants) is an abundant red algal polysaccharide, whose mechanism of catabolism by marine bacteria, however, remains largely unknown. This study reveals the catabolism of MLX by marine Bacteroidetes, promoting our understanding of the degradation and utilization of algal polysaccharides by marine bacteria. This study also sets a foundation for the biomass conversion of MLX.


Subject(s)
Flavobacteriaceae , Rhodophyta , Xylans/metabolism , Ecosystem , Flavobacteriaceae/metabolism , Polysaccharides/metabolism , Bacteroidetes/metabolism , Plants/metabolism , Rhodophyta/metabolism , Carbon/metabolism
5.
Environ Int ; 182: 108325, 2023 Dec.
Article in English | MEDLINE | ID: mdl-37995388

ABSTRACT

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.


Subject(s)
Alginates , Microbiota , Alginates/metabolism , Bacteria/genetics , Seawater/microbiology
6.
J Biol Chem ; 299(9): 105116, 2023 Sep.
Article in English | MEDLINE | ID: mdl-37524130

ABSTRACT

Xylans are polysaccharides composed of xylose and include ß1,4-xylan, ß1,3-xylan, and ß1,3/1,4-mixed-linkage xylan (MLX). MLX is widely present in marine red algae and constitutes a significant organic carbon in the ocean. Xylanases are hydrolase enzymes that play an important role in xylan degradation. While a variety of ß1,4-xylanases and ß1,3-xylanases involved in the degradation of ß1,4-xylan and ß1,3-xylan have been reported, no specific enzyme has yet been identified that degrades MLX. Herein, we report the characterization of a new MLX-specific xylanase from the marine bacterium Polaribacter sp. Q13 which utilizes MLX for growth. The bacterium secretes xylanases to degrade MLX, among which is Xyn26A, an MLX-specific xylanase that shows low sequence similarities (<27%) to ß1,3-xylanases in the glycoside hydrolase family 26 (GH26). We show that Xyn26A attacks MLX precisely at ß1,4-linkages, following a ß1,3-linkage toward the reducing end. We confirm that Xyn26A and its homologs have the same specificity and mode of action on MLX, and thus represent a new xylanase group which we term as MLXases. We further solved the structure of a representative MLXase, AlXyn26A. Structural and biochemical analyses revealed that the specificity of MLXases depends critically on a precisely positioned ß1,3-linkage at the -2/-1 subsite. Compared to the GH26 ß1,3-xylanases, we found MLXases have evolved a tunnel-shaped cavity that is fine-tuned to specifically recognize and hydrolyze MLX. Overall, this study offers a foremost insight into MLXases, shedding light on the biochemical mechanism of bacterial degradation of MLX.

7.
Mar Genomics ; 67: 101007, 2023 Feb.
Article in English | MEDLINE | ID: mdl-36682850

ABSTRACT

Marinimicrobium sp. C6131, which had the ability to degrade chitin, was isolated from deep-sea sediment of the southwest Indian Ocean. Here, the genome of strain C6131 was sequenced and the chitin metabolic pathways were constructed. The genome contained a circular chromosome of 4,207,651 bp with a G + C content of 58.50%. A total of 3471 protein-coding sequences were predicted. Gene annotation and metabolic pathway reconstruction showed that strain C6131 possessed genes and two metabolic pathways involved in chitin catabolism: the hydrolytic chitin utilization pathway initiated by chitinases and the oxidative chitin utilization pathway initiated by lytic polysaccharide monooxygenases. Chitin is the most abundant polysaccharide in the ocean. Degradation and recycling of chitin driven by marine bacteria are crucial for biogeochemical cycles of carbon and nitrogen in the ocean. The genomic information of strain C6131 revealed its genetic potential involved in chitin metabolism. The strain C6131 could grow with colloidal chitin as the sole carbon source, indicating that these genes would have functions in chitin degradation and utilization. The genomic sequence of Marinimicrobium sp. C6131 could provide fundamental information for future studies on chitin degradation, and help to improve our understanding of the chitin degradation process in deep-sea environments.


Subject(s)
Gammaproteobacteria , Genome, Bacterial , Genomics , Chitin/metabolism , Carbon
8.
Appl Environ Microbiol ; 88(23): e0155922, 2022 12 13.
Article in English | MEDLINE | ID: mdl-36394323

ABSTRACT

Alginate lyases play a vital role in the degradation of alginate, an important marine carbon source. Alginate is a complex macromolecular substrate, and the synergy of alginate lyases is important for the alginate utilization by microbes and the application of alginate lyases in biotechnology. Although many studies have focused on the synergy between different alginate lyases, the synergy between two alginate lyase domains of one alginate lyase has not been reported. Here, we report the synergism between the two catalytic domains of a novel alginate lyase, AlyC6', from the marine alginate-degrading bacterium Vibrio sp. NC2. AlyC6' contains two PL7 catalytic domains (CD1 and CD2) that have no sequence similarity. While both CD1 and CD2 are endo-lyases with the highest activity at 30°C, pH 8.0, and 1.0 M NaCl, they also displayed some different properties. CD1 was PM-specific, but CD2 was PG-specific. Compared with CD2, CD1 had higher catalytic efficiency, but lower substrate affinity. In addition, CD1 had a smaller minimal substrate than CD2, and the products from CD2 could be further degraded by CD1. These distinctions between the two domains enable them to synergize intramolecularly in alginate degradation, resulting in efficient and complete degradation of various alginate substrates. The bioinformatics analysis revealed that diverse alginate lyases have multiple catalytic domains, which are widespread, especially abundant in Flavobacteriaceae and Alteromonadales, which may secret multimodular alginate lyases for alginate degradation. This study provides new insight into bacterial alginate lyases and alginate degradation and is helpful for designing multimodular enzymes for efficient alginate depolymerization. IMPORTANCE Alginate is a major component in the cell walls of brown algae. Alginate degradation is carried out by alginate lyases. Until now, while most characterized alginate lyases contain one single catalytic domain, only a few have been shown to contain two catalytic domains. Furthermore, the synergy of alginate lyases has attracted increasing attention since it plays important roles in microbial alginate utilization and biotechnological applications. Although many studies have focused on the synergy between different alginate lyases, the synergy between two catalytic domains of one alginate lyase has not been reported. Here, a novel alginate lyase, AlyC6', with two functional alginate lyase domains was biochemically characterized. Moreover, the synergism between the two domains of AlyC6' was revealed. Additionally, the distribution of the alginate lyases with multiple alginate lyase domains was investigated based on the bioinformatics analysis. This study provides new insight into bacterial alginate lyases and alginate degradation.


Subject(s)
Polysaccharide-Lyases , Vibrio , Amino Acid Sequence , Polysaccharide-Lyases/metabolism , Vibrio/metabolism , Alginates/metabolism , Substrate Specificity
9.
Nat Commun ; 13(1): 5899, 2022 10 06.
Article in English | MEDLINE | ID: mdl-36202810

ABSTRACT

Oxidative degradation of chitin, initiated by lytic polysaccharide monooxygenases (LPMOs), contributes to microbial bioconversion of crystalline chitin, the second most abundant biopolymer in nature. However, our knowledge of oxidative chitin utilization pathways, beyond LPMOs, is very limited. Here, we describe a complete pathway for oxidative chitin degradation and its regulation in a marine bacterium, Pseudoalteromonas prydzensis. The pathway starts with LPMO-mediated extracellular breakdown of chitin into C1-oxidized chitooligosaccharides, which carry a terminal 2-(acetylamino)-2-deoxy-D-gluconic acid (GlcNAc1A). Transmembrane transport of oxidized chitooligosaccharides is followed by their hydrolysis in the periplasm, releasing GlcNAc1A, which is catabolized in the cytoplasm. This pathway differs from the known hydrolytic chitin utilization pathway in enzymes, transporters and regulators. In particular, GlcNAc1A is converted to 2-keto-3-deoxygluconate 6-phosphate, acetate and NH3 via a series of reactions resembling the degradation of D-amino acids rather than other monosaccharides. Furthermore, genomic and metagenomic analyses suggest that the chitin oxidative utilization pathway may be prevalent in marine Gammaproteobacteria.


Subject(s)
Chitin , Mixed Function Oxygenases , Amino Acids , Bacteria/metabolism , Chitin/metabolism , Mixed Function Oxygenases/metabolism , Monosaccharides , Phosphates , Polysaccharides/metabolism
10.
Microbiol Spectr ; 10(5): e0069122, 2022 10 26.
Article in English | MEDLINE | ID: mdl-36040174

ABSTRACT

Diaminopimelic acid (DAP) is a unique component of the cell wall of Gram-negative bacteria. It is also an important component of organic matter and is widely utilized by microbes in the world's oceans. However, neither DAP concentrations nor marine DAP-utilizing microbes have been investigated. Here, DAP concentrations in seawater were measured and the diversity of marine DAP-utilizing bacteria and the mechanisms for their DAP metabolism were investigated. Free DAP concentrations in seawater, from surface to a 5,000 m depth, were found to be between 0.61 µM and 0.96 µM in the western Pacific Ocean. DAP-utilizing bacteria from 20 families in 4 phyla were recovered from the western Pacific seawater and 14 strains were further isolated, in which Pseudomonadota bacteria were dominant. Based on genomic and transcriptomic analyses combined with gene deletion and in vitro activity detection, DAP decarboxylase (LysA), which catalyzes the decarboxylation of DAP to form lysine, was found to be a key and specific enzyme involved in DAP metabolism in the isolated Pseudomonadota strains. Interrogation of the Tara Oceans database found that most LysA-like sequences (92%) are from Pseudomonadota, which are widely distributed in multiple habitats. This study provides an insight into DAP metabolism by marine bacteria in the ocean and contributes to our understanding of the mineralization and recycling of DAP by marine bacteria. IMPORTANCE DAP is a unique component of peptidoglycan in Gram-negative bacterial cell walls. Due to the large number of marine Gram-negative bacteria, DAP is an important component of marine organic matter. However, it remains unclear how DAP is metabolized by marine microbes. This study investigated marine DAP-utilizing bacteria by cultivation and bioinformational analysis and examined the mechanism of DAP metabolism used by marine bacteria. The results demonstrate that Pseudomonadota bacteria are likely to be an important DAP-utilizing group in the ocean and that DAP decarboxylase is a key enzyme involved in DAP metabolism. This study also sheds light on the mineralization and recycling of DAP driven by bacteria.


Subject(s)
Carboxy-Lyases , Diaminopimelic Acid , Gram-Negative Bacteria , Peptidoglycan , Bacteria/genetics , Bacteria/metabolism , Carboxy-Lyases/metabolism , Diaminopimelic Acid/metabolism , Gram-Negative Bacteria/metabolism , Lysine/metabolism , Peptidoglycan/metabolism
11.
iScience ; 25(8): 104680, 2022 Aug 19.
Article in English | MEDLINE | ID: mdl-35942087

ABSTRACT

Hadal ocean biosphere, that is, the deepest part of the world's oceans, harbors a unique microbial community, suggesting a potential uncovered co-occurring virioplankton assemblage. Herein, we reveal the unique virioplankton assemblages of the Challenger Deep, comprising 95,813 non-redundant viral contigs from the surface to the hadal zone. Almost all of the dominant viral contigs in the hadal zone were unclassified, potentially related to Alteromonadales and Oceanospirillales. 2,586 viral auxiliary metabolic genes from 132 different KEGG orthologous groups were mainly related to the carbon, nitrogen, sulfur, and arsenic metabolism. Lysogenic viral production and integrase genes were augmented in the hadal zone, suggesting the prevalence of viral lysogenic life strategy. Abundant rve genes in the hadal zone, which function as transposase in the caudoviruses, further suggest the prevalence of viral-mediated horizontal gene transfer. This study provides fundamental insights into the virioplankton assemblages of the hadal zone, reinforcing the necessity of incorporating virioplankton into the hadal biogeochemical cycles.

12.
Commun Biol ; 5(1): 705, 2022 07 14.
Article in English | MEDLINE | ID: mdl-35835984

ABSTRACT

Members of the marine Roseobacter group are ubiquitous in global oceans, but their cold-adaptive strategies have barely been studied. Here, as represented by Loktanella salsilacus strains enriched in polar regions, we firstly characterized the metabolic features of a cold-adapted Roseobacter by multi-omics, enzyme activities, and carbon utilization procedures. Unlike in most cold-adapted microorganisms, the TCA cycle is enhanced by accumulating more enzyme molecules, whereas genes for thiosulfate oxidation, sulfate reduction, nitrate reduction, and urea metabolism are all expressed at lower abundance when L. salsilacus was growing at 5 °C in comparison with higher temperatures. Moreover, a carbon-source competition experiment has evidenced the preferential use of glucose rather than sucrose at low temperature. This selective utilization is likely to be controlled by the carbon source uptake and transformation steps, which also reflects an economic calculation balancing energy production and functional plasticity. These findings provide a mechanistic understanding of how a Roseobacter member and possibly others as well counteract polar constraints.


Subject(s)
Roseobacter , Carbon/metabolism , Citric Acid Cycle , Oceans and Seas , Roseobacter/genetics , Roseobacter/metabolism , Temperature
13.
Mar Genomics ; 62: 100935, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35246307

ABSTRACT

The Mariana Trench is the deepest site on earth with diverse extreme conditions such as high hydrostatic pressure, low temperature and lack of light. Organisms surviving in this extreme environment and their life strategies have been largely uninvestigated. Here, we report the complete genome of Marinomonas profundi M1K-6T, isolated from the Mariana Trench deep seawater. The assembled genome comprised 3,648,059 bp without any plasmid. Gene annotation showed that strain M1K-6T possesses a series of genes encoding cold-shock proteins, DEAD box RNA helicase and enzymes for biosynthesis of unsaturated fatty acids, implying its high cold tolerance. Abundant genes responsible for transports of ion, branched-chain amino acids and organic compatible solutes were detected, which could maintain cellular osmotic balance disturbed by high hydrostatic pressure. In addition, detected genes (related to storage carbon, transport systems and two-component regulatory systems) could help strain M1K-6T to improve its ecological fitness in the deep-sea microaerobic and nutrient-limiting environments. Genomic information on M. profundi M1K-6T, provides insights into the adaptation strategies of Marinomonas spp. in the extreme deep-sea environment of the Mariana Trench.


Subject(s)
Marinomonas , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Genomics , Marinomonas/genetics , Pacific Ocean , Phylogeny , RNA, Ribosomal, 16S/genetics , Seawater
14.
Mar Drugs ; 20(3)2022 Feb 24.
Article in English | MEDLINE | ID: mdl-35323464

ABSTRACT

Chitooligosaccharides (COSs) have been widely used in agriculture, medicine, cosmetics, and foods, which are commonly prepared from chitin with chitinases. So far, while most COSs are prepared from colloidal chitin, chitinases used in preparing COSs directly from natural crystalline chitin are less reported. Here, we characterize three chitinases, which were identified from the marine bacterium Pseudoalteromonas flavipulchra DSM 14401T, with an ability to degrade crystalline chitin into (GlcNAc)2 (N,N'-diacetylchitobiose). Strain DSM 14401 can degrade the crystalline α-chitin in the medium to provide nutrients for growth. Genome and secretome analyses indicate that this strain secretes six chitinolytic enzymes, among which chitinases Chia4287, Chib0431, and Chib0434 have higher abundance than the others, suggesting their importance in crystalline α-chitin degradation. These three chitinases were heterologously expressed, purified, and characterized. They are all active on crystalline α-chitin, with temperature optima of 45-50 °C and pH optima of 7.0-7.5. They are all stable at 40 °C and in the pH range of 5.0-11.0. Moreover, they all have excellent salt tolerance, retaining more than 92% activity after incubation in 5 M NaCl for 10 h at 4 °C. When acting on crystalline α-chitin, the main products of the three chitinases are all (GlcNAc)2, which suggests that chitinases Chia4287, Chib0431, and Chib0434 likely have potential in direct conversion of crystalline chitin into (GlcNAc)2.


Subject(s)
Bacterial Proteins/chemistry , Chitin/chemistry , Chitinases/chemistry , Disaccharides/chemistry , Pseudoalteromonas/enzymology , Bacterial Proteins/isolation & purification , Chitinases/isolation & purification , Genome, Bacterial , Pseudoalteromonas/genetics , Sodium Chloride/chemistry
15.
Environ Microbiol ; 24(1): 98-109, 2022 01.
Article in English | MEDLINE | ID: mdl-34913576

ABSTRACT

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.


Subject(s)
Genomics , Pseudoalteromonas , Antarctic Regions , Geography , Phylogeny , Pseudoalteromonas/genetics , RNA, Ribosomal, 16S/genetics
17.
Microbiome ; 9(1): 207, 2021 10 16.
Article in English | MEDLINE | ID: mdl-34654476

ABSTRACT

BACKGROUND: Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth's surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled. RESULTS: Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans. CONCLUSIONS: Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels. Video Abstract.


Subject(s)
Seawater , Oceans and Seas , Phylogeny , Sulfides , Sulfonium Compounds
18.
Mar Genomics ; 59: 100874, 2021 Oct.
Article in English | MEDLINE | ID: mdl-34493388

ABSTRACT

Pelagovum pacificum SM1903T, belonging to a novel genus of the family Rhodobacteraceae, was isolated from the surface seawater of the Mariana Trench. Here, we report the first complete genome sequence of the novel genus Pelagovum. The genome of strain SM1903T consists of a circular chromosome of 4,040,866 bp and two plasmids of 41,363 bp and 9705 bp, respectively. Gene annotation and metabolic pathway analyses showed that strain SM1903T possesses a series of genes related to adaptation to marine oligotrophic environments, which are involved in utilization of aromatic compounds, allantoin, and alkylphosphonate, and second messenger signaling in response to the oligotrophic stress. This strain also contains a variety of genes involved in coping with other stresses including osmotic stress, oxidative stress, cold shock, and heat shock. These features would assist this strain to survive under the natural nutrient limitation and other stresses from the environment. The genome of strain SM1903T of the novel genus Pelagovum would deepen our knowledge on marine bacterioplankton and their adaption strategies to marine oligotrophic environments.


Subject(s)
Genome, Bacterial , Rhodobacteraceae , Base Composition , Phylogeny , Rhodobacteraceae/genetics , Seawater
19.
Antonie Van Leeuwenhoek ; 114(7): 947-955, 2021 Jul.
Article in English | MEDLINE | ID: mdl-33864544

ABSTRACT

A novel Gram-negative, rod-shaped, aerobic, oxidase-positive and catalase-negative bacterium, designated strain SM1970T, was isolated from a seawater sample collected from the Mariana Trench. Strain SM1970T grew at 15-37 oC and with 1-5% (w/v) NaCl. It hydrolyzed colloidal chitin, agar and casein but did not reduce nitrate to nitrite. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain SM1970T formed a distinct lineage close to the genus Catenovulum within the family Alteromonadaceae, sharing the highest sequence similarity (93.6%) with type strain of Catenovulum maritimum but < 93.0% sequence similarity with those of other known species in the class Gammaproteobacteria. The major fatty acids of strain SM1970T were summed feature 3 (C16: 1 ω7c and/or C16: 1 ω6c), C16: 0 and summed feature 8 (C18: 1 ω7c and/or C18: 1 ω6c). The major polar lipids of the strain included phosphatidylethanolamine and phosphatidylglycerol and its main respiratory quinone was ubiquinone 8. The draft genome of strain SM1970T consisted of 77 scaffolds and was 4,172,146 bp in length, containing a complete set of genes for chitin degradation. The average amino acid identity (AAI) values between SM1970T and type strains of known Catenovulum species were 56.6-57.1% while the percentage of conserved proteins (POCP) values between them were 28.5-31.5%. The genomic DNA G + C content of strain SM1970T was 40.1 mol%. On the basis of the polyphasic analysis, strain SM1970T is considered to represent a novel species in a novel genus of the family Alteromonadaceae, for which the name Marinifaba aquimaris is proposed with the type strain being SM1970T (= MCCC 1K04323T = KCTC 72844T).


Subject(s)
Alteromonadaceae , Chitin , Alteromonadaceae/genetics , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids/analysis , Phospholipids/analysis , Phylogeny , RNA, Ribosomal, 16S/genetics , Seawater , Sequence Analysis, DNA
20.
Antonie Van Leeuwenhoek ; 114(6): 787-798, 2021 Jun.
Article in English | MEDLINE | ID: mdl-33782795

ABSTRACT

Two Gram-stain-negative bacterial strains, SM1969T and SM1979T, were isolated from coastal surface seawater of Qingdao, China. They were taxonomically characterized by the phylogenetic, genomic, chemotaxonomic and phenotypic analyses. The two strains shared 97.0% 16S rRNA gene sequence similarity with each other and the highest similarity (96.8-97.5%) with type strains of six species in the genera Shimia, Tritonibacter and Tropicibacter in the Roseobacter group of the family Rhodobacteraceae. In the phylogenetic tree based on single-copy orthologous clusters (OCs), both strains clustered with known species of the genus Tritonibacter and together formed a separate branch adjacent to Tritonibacter ulvae. Although sharing many chemotaxonomic and phenotypic characteristics, the two strains could be differentiated from each other and closely related species by numerous traits. Particularly, strain SM1969T was found to have a DMSP lyase coding gene dddW in its genome and have the ability to produce DMS from DMSP while strain SM1979T was not. The average nucleotide identity and in silico DNA-DNA hybridization values between strains SM1969T and SM1979T and type strains of closely related species were all below the thresholds to discriminate bacterial species, demonstrating that they constitute two new species in the genus Tritonibacter. The names Tritonibacter aquimaris sp. nov. and Tritonibacter litoralis sp. nov. are proposed for the two new species, with type strains being SM1969T (= MCCC 1K04320T = KCTC 72843T) and SM1979T (= MCCC 1K04321T = KCTC 72842T), respectively.


Subject(s)
Rhodobacteraceae , Roseobacter , Bacterial Typing Techniques , Base Composition , DNA, Bacterial/genetics , Fatty Acids , Nucleic Acid Hybridization , Phospholipids , Phylogeny , RNA, Ribosomal, 16S/genetics , Rhodobacteraceae/genetics , Roseobacter/genetics , Seawater , Sequence Analysis, DNA
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