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1.
J Hazard Mater ; 479: 135638, 2024 Nov 05.
Article in English | MEDLINE | ID: mdl-39217937

ABSTRACT

Microplastics in aquatic ecosystems harbor numerous microorganisms, including pathogenic species. The ingestion of these microplastics by commercial fish poses a threat to the ecosystem and human livelihood. Coastal lagoons are highly vulnerable to microplastic and microbiological pollution, yet limited understanding of the risks complicates management. Here, we present the main bacterial groups, including potentially pathogenic species, identified on microplastics in waters, sediments, and commercial fish from Ciénaga Grande de Santa Marta (CGSM), the largest coastal lagoon in Colombia. DNA metabarcoding allowed identifying 1760 bacterial genera on microplastics, with Aeromonas and Acinetobacter as the most frequent and present in all three matrices. The greatest bacterial richness and diversity were recorded on microplastics from sediments, followed by waters and fish. Biochemical analyses yielded 19 species of potentially pathogenic culturable bacteria on microplastics. Aeromonas caviae was the most frequent and, along with Pantoea sp., was found on microplastics in all three matrices. Enterobacter roggenkampii and Pseudomonas fluorescens were also found on microplastics from waters and fish. We propose management strategies for an Early Warning System against microbiological and microplastic pollution risks in coastal lagoons, illustrated by CGSM. This includes forming inter-institutional alliances for research and monitoring, accompanied by strengthening governance and health infrastructures.


Subject(s)
Bacteria , Geologic Sediments , Microplastics , Animals , Geologic Sediments/microbiology , Bacteria/classification , Bacteria/genetics , Bacteria/isolation & purification , Fishes/microbiology , Water Pollutants, Chemical/analysis , Colombia , Environmental Monitoring , Water Microbiology , Seawater/microbiology
2.
Nature ; 633(8030): 587-593, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39261723

ABSTRACT

The biological pump supplies carbon to the oceans' interior, driving long-term carbon sequestration and providing energy for deep-sea ecosystems1,2. Its efficiency is set by transformations of newly formed particles in the euphotic zone, followed by vertical flux attenuation via mesopelagic processes3. Depth attenuation of the particulate organic carbon (POC) flux is modulated by multiple processes involving zooplankton and/or microbes4,5. Nevertheless, it continues to be mainly parameterized using an empirically derived relationship, the 'Martin curve'6. The derived power-law exponent is the standard metric used to compare flux attenuation patterns across oceanic provinces7,8. Here we present in situ experimental findings from C-RESPIRE9, a dual particle interceptor and incubator deployed at multiple mesopelagic depths, measuring microbially mediated POC flux attenuation. We find that across six contrasting oceanic regimes, representing a 30-fold range in POC flux, degradation by particle-attached microbes comprised 7-29 per cent of flux attenuation, implying a more influential role for zooplankton in flux attenuation. Microbial remineralization, normalized to POC flux, ranged by 20-fold across sites and depths, with the lowest rates at high POC fluxes. Vertical trends, of up to threefold changes, were linked to strong temperature gradients at low-latitude sites. In contrast, temperature played a lesser role at mid- and high-latitude sites, where vertical trends may be set jointly by particle biochemistry, fragmentation and microbial ecophysiology. This deconstruction of the Martin curve reveals the underpinning mechanisms that drive microbially mediated POC flux attenuation across oceanic provinces.


Subject(s)
Aquatic Organisms , Carbon Cycle , Carbon , Ecosystem , Oceans and Seas , Seawater , Animals , Carbon/metabolism , Carbon Sequestration , Seawater/chemistry , Seawater/microbiology , Zooplankton/metabolism , Temperature , Aquatic Organisms/metabolism
3.
Curr Microbiol ; 81(11): 365, 2024 Sep 18.
Article in English | MEDLINE | ID: mdl-39292287

ABSTRACT

Benthic habitats are the largest habitats on Earth, being essential for marine ecosystem functioning. Benthic habitats are particularly vulnerable towards pollution and anthropogenetic influence due to general oligotrophic nature. We, therefore, simulated pollution events involving nitrate and sulphate, in combination with organic carbon. We then observed the microbiota composition the following month. Surprisingly, upon nitrate addition, an abrupt response was observed between two and three weeks after the pollution event. We observed a threefold reduction in species richness, with a dominance of the genus Pseudarchobacter within the Campylobacteriota phylum, concurring with a decrease in nitrification potential and an increase in Dissimilatory Nitrate Reduction to Ammonium (DNRA) and a regain in denitrification. Likewise, addition of sulphate contributed to a delayed response with reduction in species richness albeit weaker than for nitrate, leading to a shift towards potential spore-forming Firmicutes. There was also an increase in DNRA, but only for the oxic conditions, concurring with a regain in sulphate reductio and denitrification. For the nitrate addition experiments, the delay in response could potentially be attributed to the genus Pseudarchobacter which rely on sulphides for denitrification, while for the sulphate addition experiments, the delayed response might be explained by the germination of spores. The late increase of DNRA may indicate a shift towards a different metabolic regime for nitrogen. In conclusion, our microcosm experiments revealed delayed abrupt microbiota shifts resembling tipping points that can potentially be overlooked in natural ecosystems.


Subject(s)
Bacteria , Microbiota , Nitrates , Seawater , Bacteria/classification , Bacteria/genetics , Bacteria/metabolism , Bacteria/isolation & purification , Nitrates/metabolism , Seawater/microbiology , Sulfates/metabolism , Ecosystem
4.
Environ Monit Assess ; 196(10): 939, 2024 Sep 17.
Article in English | MEDLINE | ID: mdl-39287716

ABSTRACT

Microplastics (MPs) are a potential threat to the marine environment and its associated ecosystem functions. Earlier investigations revealed that the microbiome plays a crucial role in deciding the fate of MPs in the environment. Further studies also highlighted the influences of environment and polymer types on the plastisphere microbiome. Nevertheless, the major factor that determines the plastisphere microbiome remains elusive. Thus, we examined the publicly available marine plastisphere data generated from polyethylene (PE), polypropylene (PP), and polystyrene (PS), collected from three different locations to identify the importance of environment and/or polymer types in shaping the microbiome. The beta diversity analyses showed a clear distinction between samples collected from different locations. The PERMANOVA results illustrated a significant influence of environment and sample type (control/PE/PP/PS) on the microbial communities. However, the influence of sample type on microbial diversity was not significant (P-value > 0.05) when the control samples were removed from the dataset but the environment remained a significant factor (P-value < 0.05). Further, the differential abundance analyses explicitly showed the abundance of many bacterial taxa to be significantly influenced (adjusted P-value < 0.05) by the locations rather than the polymer types. The validation analysis also supports the findings. Thus, this study suggests that both the surrounding environment and polymer types determine the microbial communities on marine MPs, but the role of the environment in shaping the microbial composition is greater than that of polymer types.


Subject(s)
Environmental Monitoring , Microbiota , RNA, Ribosomal, 16S , Environmental Monitoring/methods , RNA, Ribosomal, 16S/genetics , Water Pollutants, Chemical/analysis , Microplastics , Bacteria/genetics , Bacteria/classification , Bacteria/isolation & purification , Seawater/microbiology , Polyethylene , Polypropylenes , Polystyrenes , Water Microbiology
5.
Nature ; 633(8031): 823-827, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39322731

ABSTRACT

Primary production in the sunlit surface ocean is regulated by the supply of key nutrients, primarily nitrate, phosphate and iron (Fe), required by phytoplankton to fix carbon dioxide into biomass1-3. Below the surface ocean, remineralization of sinking organic matter rapidly regenerates nutrients, and microbial metabolism in the upper mesopelagic 'twilight zone' (200-500 m) is thought to be limited by the delivery of labile organic carbon4,5. However, few studies have examined the role of nutrients in shaping microbial production in the mesopelagic6-8. Here we report the distribution and uptake of siderophores, biomarkers for microbial Fe deficiency9 across a meridional section of the eastern Pacific Ocean. Siderophore concentrations are high not only in chronically Fe-limited surface waters but also in the twilight zone underlying the North and South Pacific subtropical gyres, two key ecosystems for the marine carbon cycle. Our findings suggest that bacterial Fe deficiency owing to low Fe availability is probably characteristic of the twilight zone in several large ocean basins, greatly expanding the region of the marine water column in which nutrients limit microbial metabolism, with potential implications for ocean carbon storage.


Subject(s)
Iron , Seawater , Siderophores , Iron/metabolism , Pacific Ocean , Seawater/chemistry , Seawater/microbiology , Siderophores/metabolism , Carbon Cycle , Phytoplankton/metabolism , Bacteria/metabolism , Iron Deficiencies , Carbon/metabolism , Carbon/analysis , Ecosystem
6.
Mar Drugs ; 22(9)2024 Aug 24.
Article in English | MEDLINE | ID: mdl-39330262

ABSTRACT

Arthrospira platensis holds promise for biotechnological applications due to its rapid growth and ability to produce valuable bioactive compounds like phycocyanin (PC). This study explores the impact of salinity and brewery wastewater (BWW) on the mixotrophic cultivation of A. platensis. Utilizing BWW as an organic carbon source and seawater (SW) for salt stress, we aim to optimize PC production and biomass composition. Under mixotrophic conditions with 2% BWW and SW, A. platensis showed enhanced biomass productivity, reaching a maximum of 3.70 g L-1 and significant increases in PC concentration. This study also observed changes in biochemical composition, with elevated protein and carbohydrate levels under salt stress that mimics the use of seawater. Mixotrophic cultivation with BWW and SW also influenced the FAME profile, enhancing the content of C16:0 and C18:1 FAMES. The purity (EP of 1.15) and yield (100 mg g-1) of PC were notably higher in mixotrophic cultures, indicating the potential for commercial applications in food, cosmetics, and pharmaceuticals. This research underscores the benefits of integrating the use of saline water with waste valorization in microalgae cultivation, promoting sustainability and economic efficiency in biotechnological processes.


Subject(s)
Biomass , Phycocyanin , Salt Stress , Spirulina , Spirulina/metabolism , Spirulina/growth & development , Spirulina/drug effects , Microalgae/growth & development , Microalgae/metabolism , Microalgae/drug effects , Salinity , Seawater/microbiology , Seawater/chemistry , Wastewater/chemistry
7.
ISME J ; 18(1)2024 Jan 08.
Article in English | MEDLINE | ID: mdl-39244747

ABSTRACT

Microbial chemoautotroph-heterotroph interactions may play a pivotal role in the cycling of carbon in the deep ocean, reminiscent of phytoplankton-heterotroph associations in surface waters. Nitrifiers are the most abundant chemoautotrophs in the global ocean, yet very little is known about nitrifier metabolite production, release, and transfer to heterotrophic microbial communities. To elucidate which organic compounds are released by nitrifiers and potentially available to heterotrophs, we characterized the exo- and endometabolomes of the ammonia-oxidizing archaeon Nitrosopumilus adriaticus CCS1 and the nitrite-oxidizing bacterium Nitrospina gracilis Nb-211. Nitrifier endometabolome composition was not a good predictor of exometabolite availability, indicating that metabolites were predominately released by mechanisms other than cell death/lysis. Although both nitrifiers released labile organic compounds, N. adriaticus preferentially released amino acids, particularly glycine, suggesting that its cell membranes might be more permeable to small, hydrophobic amino acids. We further initiated co-culture systems between each nitrifier and a heterotrophic alphaproteobacterium, and compared exometabolite and transcript patterns of nitrifiers grown axenically to those in co-culture. In particular, B vitamins exhibited dynamic production and consumption patterns in nitrifier-heterotroph co-cultures. We observed an increased production of vitamin B2 and the vitamin B12 lower ligand dimethylbenzimidazole by N. adriaticus and N. gracilis, respectively. In contrast, the heterotroph likely produced vitamin B5 in co-culture with both nitrifiers and consumed the vitamin B7 precursor dethiobiotin when grown with N. gracilis. Our results indicate that B vitamins and their precursors could play a particularly important role in governing specific metabolic interactions between nitrifiers and heterotrophic microbes in the ocean.


Subject(s)
Nitrification , Seawater , Seawater/microbiology , Oceans and Seas , Nitrites/metabolism , Heterotrophic Processes , Microbial Interactions , Metabolome , Coculture Techniques , Ammonia/metabolism
8.
Environ Microbiol Rep ; 16(5): e70005, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39285802

ABSTRACT

In nature, the number of genome or chromosome copies within cells (ploidy) can vary between species and environmental conditions, potentially influencing how organisms adapt to changing environments. Although ploidy levels cannot be easily determined by standard genome sequencing, understanding ploidy is crucial for the quantitative interpretation of molecular data. Cyanobacteria are known to contain haploid, oligoploid, and polyploid species. The smallest cyanobacteria, picocyanobacteria (less than 2 µm in diameter), have a widespread distribution ranging from marine to freshwater environments, contributing significantly to global primary production. In this study, we determined the ploidy level of genetically and physiologically diverse brackish picocyanobacteria isolated from the Baltic Sea using a qPCR assay targeting the rbcL gene. The strains contained one to four genome copies per cell. The ploidy level was not linked with phylogeny based on the identity of the 16S rRNA gene. The variation of ploidy among the brackish strains was lower compared to what has been reported for freshwater strains and was more similar to what has been reported for marine strains. The potential ecological advantage of polyploidy among picocyanobacteria has yet to be described. Our study highlights the importance of considering ploidy to interpret the abundance and adaptation of brackish picocyanobacteria.


Subject(s)
Cyanobacteria , Phylogeny , Ploidies , RNA, Ribosomal, 16S , Seawater , Seawater/microbiology , Cyanobacteria/genetics , Cyanobacteria/classification , Cyanobacteria/isolation & purification , RNA, Ribosomal, 16S/genetics , DNA, Bacterial/genetics , Oceans and Seas
9.
Microb Biotechnol ; 17(9): e70009, 2024 Sep.
Article in English | MEDLINE | ID: mdl-39264362

ABSTRACT

Carotenoids are natural pigments utilized as colourants and antioxidants across food, pharmaceutical and cosmetic industries. They exist in carbon chain lengths of C30, C40, C45 and C50, with C40 variants being the most common. Bacterioruberin (BR) and its derivatives are part of the less common C50 carotenoid group, synthesized primarily by halophilic archaea. This study analysed the compositional characteristics of BR extract (BRE) isolated from 'Haloferax marinum' MBLA0078, a halophilic archaeon isolated from seawater near Yeoungheungdo Island in the Republic of Korea, and investigated its antioxidant activity and protective effect on lipopolysaccharide (LPS)-induced C2C12 myotube atrophy. The main components of BRE included all-trans-BR, monoanhydrobacterioruberin, 2-isopentenyl-3,4-dehydrorhodopin and all-trans-bisanhydrobacterioruberin. BRE exhibited higher antioxidant activity and DNA nicking protection activity than other well-known C40 carotenoids, such as ß-carotene, lycopene and astaxanthin. In C2C12 myotubes, LPS treatment led to a reduction in myotube diameter and number, as well as the hypertranscription of the muscle-specific ubiquitin ligase MAFbx and MuRF1. BRE mitigated these changes by activating the Akt/mTOR pathway. Furthermore, BRE abolished the elevated cellular reactive oxygen species levels and the inflammation response induced by LPS. This study demonstrated that 'Hfx. marinum' is an excellent source of natural microbial C50 carotenoids with strong antioxidant capacity and may offer potential protective effects against muscle atrophy.


Subject(s)
Antioxidants , Carotenoids , Lipopolysaccharides , Muscle Fibers, Skeletal , Antioxidants/pharmacology , Animals , Mice , Muscle Fibers, Skeletal/drug effects , Muscle Fibers, Skeletal/metabolism , Cell Line , Carotenoids/pharmacology , Republic of Korea , Seawater/microbiology
10.
Sci Data ; 11(1): 994, 2024 Sep 12.
Article in English | MEDLINE | ID: mdl-39266528

ABSTRACT

The Changjiang Estuary and adjacent East China Sea are well-known hypoxic aquatic environments. Eutrophication-driven hypoxia frequently occurs in coastal areas, posing a major threat to the ecological environment, including altering community structure and metabolic processes of marine organisms, and enhancing diversion of energy shunt into microbial communities. However, the responses of microbial communities and their metabolic pathways to coastal hypoxia remain poorly understood. Here, we studied the microbial communities collected from spatiotemporal samplings using metagenomic sequencing in the Changjiang Estuary and adjacent East China Sea. This generated 1.31 Tbp of metagenomics data, distributed across 103 samples corresponding to 8 vertical profiles. We further reported 1,559 metagenome-assembled genomes (MAGs), of which 508 were high-quality MAGs (Completeness > 90% and Contamination < 10%). Phylogenomic analysis classified them into 181 archaeal and 1,378 bacterial MAGs. These results provided a valuable metagenomic dataset available for further investigation of the effects of hypoxia on marine microorganisms.


Subject(s)
Archaea , Metagenome , China , Archaea/genetics , Bacteria/genetics , Bacteria/classification , Oxygen , Seawater/microbiology , Phylogeny , Metagenomics , Oceans and Seas , Microbiota
11.
Sci Total Environ ; 953: 176075, 2024 Nov 25.
Article in English | MEDLINE | ID: mdl-39244045

ABSTRACT

Both petroleum hydrocarbons (PHCs) from oil pollution and colored dissolved organic matter (CDOM) have great influences on the marine microbial community as carbon source factors. However, their combined effects and the specific influence patterns have been kept unclear. This study selected the northeastern South China Sea (NSCS), a typical oil contaminated area, and investigated the characteristics of oil-degrading microbiota in the seawaters by high-throughput sequencing and the relationships with PHCs and CDOM as well as other environmental factors. The results showed the oil pollution had induced the enrichment of oil-degrading bacteria and oil-degrading functional genes, resulting in the core function of oil-degrading microbiota for shaping the microbial community. The Mantel test indicated carbon source factors played the dominant role in shaping the oil-degrading microbiota, compared with geographical distance and other non­carbon source factors. The influence patterns and strength of PHCs and CDOM on oil-degrading microbiota were further comprehensively analyzed. PHCs played a driving role in the differentiation of oil-degrading microbiota, while CDOM played a stabilizing role for the community similarity. The constructed structural equation model confirmed their distinct influence patterns and also explored the mediating effects of bulk organic carbon. This work not only revealed the important impact of oil pollution on marine microbial communities, but also made people realize the self-regulation ability of the marine environment through the endogenous organic matter.


Subject(s)
Hydrocarbons , Microbiota , Petroleum , Water Pollutants, Chemical , Petroleum/metabolism , Hydrocarbons/metabolism , Water Pollutants, Chemical/metabolism , Water Pollutants, Chemical/analysis , China , Seawater/microbiology , Petroleum Pollution , Biodegradation, Environmental , Bacteria/metabolism , Bacteria/classification , Environmental Monitoring
12.
NPJ Biofilms Microbiomes ; 10(1): 78, 2024 Sep 03.
Article in English | MEDLINE | ID: mdl-39227595

ABSTRACT

Protists are less studied for their role and diversity in ecosystems. Notably, protists have played and still play an important role in microbialites. Microbialites, or lithified microbial mats, represent the oldest evidence of fossil biofilms (~3.5 Gyr). Modern microbialites may offer a unique proxy to study the potential role of protists within a geological context. We examined protist diversity in freshwater (Kelly and Pavilion Lake in British Columbia, Canada) and marine (Highborne Cay, Bahamas) to hypersaline (Shark Bay, Australia) microbialites to decipher their geomicrobiological role. The freshwater microbialite communities were clearly distinct from their marine and hypersaline counterparts. Chlorophytes had higher numerical abundance in freshwater microbialites; whereas pennate diatoms dominated numerically in marine microbialites. Despite the differences, protists across ecosystems may have adopted similar roles and functions. We suggest a consistent biogeochemical role of protists across microbialites globally; but that salinity may shape protist composition and evolution in these ecosystems.


Subject(s)
Ecosystem , Salinity , British Columbia , Eukaryota/classification , Biodiversity , Fresh Water/microbiology , Biofilms/growth & development , Seawater/microbiology , Australia , Diatoms/growth & development , Geologic Sediments/microbiology
13.
Article in English | MEDLINE | ID: mdl-39264709

ABSTRACT

A Gram-stain-negative, yellow-pigmented, and strictly aerobic bacterium, designated as strain MSW5T, was isolated from seawater of the Yellow Sea in South Korea. The cells were non-motile rods exhibiting oxidase- and catalase-positive activities. Growth was observed at 15-25 °C (optimum, 25 °C) and pH 5.0-9.0 (optimum, pH 7.0-8.0) and in the presence of 1.0-5.0% (w/v) NaCl (optimum, 2.0%). Menaquinone-6 was the sole respiratory quinone, and iso-C15 : 0, summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c), iso-C15 : 0 3-OH, and C15 : 1 ω6c were the major cellular fatty acids. Major polar lipids included phosphatidylethanolamine, two unidentified aminolipids, and three unidentified lipids. Phylogenetic analyses based on 16S rRNA gene sequences and 92 concatenated core protein sequences revealed that strain MSW5T formed a distinct lineage within the genus Polaribacter. The genome of strain MSW5T was 3582 kb in size with a 29.1 mol% G+C content. Strain MSW5T exhibited the highest similarity to Polaribacter atrinae WP25T, with a 97.9% 16S rRNA gene sequence similarity. However, the average nucleotide identity and digital DNA-DNA hybridization values were 79.4 and 23.3%, respectively, indicating that strain MSW5T represents a novel species. Based on its phenotypic, chemotaxonomic, and phylogenetic characteristics, strain MSW5T is proposed to represent a novel species, with the name Polaribacter ponticola sp. nov. The type strain is MSW5T (=KACC 22340T=NBRC 116025T). In addition, whole genome sequence comparisons and phenotypic features suggested that Polaribacter sejongensis and Polaribacter undariae belong to the same species, with P. undariae proposed as a later heterotypic synonym of P. sejongensis. An emended description of Polaribacter sejongensis is also proposed.


Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Phylogeny , RNA, Ribosomal, 16S , Seawater , Sequence Analysis, DNA , Vitamin K 2 , RNA, Ribosomal, 16S/genetics , Fatty Acids/analysis , Seawater/microbiology , Republic of Korea , DNA, Bacterial/genetics , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , Phosphatidylethanolamines , Nucleic Acid Hybridization , Bacteroidetes/genetics , Bacteroidetes/classification , Bacteroidetes/isolation & purification , Phospholipids/analysis , Phospholipids/chemistry
15.
Article in English | MEDLINE | ID: mdl-39235837

ABSTRACT

Two bacterial strains, Y60-23T and HN-65T, were isolated from marine sediment samples collected from Xiaoshi Island, Weihai, and Dongzhai Harbour, Haikou, PR China, respectively. Based on the 16S rRNA gene sequences, strain Y60-23T exhibited 96.0% similarity to its most related type strain Hyphobacterium vulgare KCTC 52487T, while strain HN-65T exhibited 97.3% similarity to its most related type strain Hyphobacterium indicum 2ED5T. The 16S rRNA gene sequence similarity between the two strains was 95.8%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains Y60-23T and HN-65T belonged to the genus Hyphobacterium. Cells of strains Y60-23T and HN-65T were rod-shaped, Gram-stain-negative, aerobic, non-motile, prosthecate and multiplied by binary fission. The major cellular fatty acids (>10.0%) of strain Y60-23T were C18 : 1 ω7c and C17 : 0, while those of strain HN-65T were iso-C17 : 1 ω9c, iso-C17 : 0 and C18 : 1 ω7c. The major respiratory quinone in both strains was ubiquinone-10 (Q-10) and the major polar lipids were monoglycosyl diglyceride, sulfoquinovosyl diacylglycerol and glucuronopyranosyl diglyceride. The genomic DNA G+C contents of strains Y60-23T and HN-65T were 63.9 and 60.7 mol%, respectively. The average nucleotide identity value between the two strains was 72.1% and the DNA-DNA hybridization value was 18.4%, clearly distinguishing them from each other. According to the results of the phenotypic, chemotaxonomic, phylogenetic and genomic analyses, the two strains represented two novel species within the genus Hyphobacterium, for which the names Hyphobacterium marinum sp. nov. and Hyphobacterium lacteum sp. nov. were proposed with the type strains Y60-23T (=MCCC 1H01433T=KCTC 8172T) and HN-65T (=MCCC 1H01434T=KCTC 8169T), respectively.


Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Geologic Sediments , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Geologic Sediments/microbiology , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , Fatty Acids/analysis , DNA, Bacterial/genetics , China , Hyphomicrobiaceae/genetics , Hyphomicrobiaceae/classification , Hyphomicrobiaceae/isolation & purification , Nucleic Acid Hybridization , Seawater/microbiology , Ubiquinone/analogs & derivatives , Phospholipids/analysis
16.
Article in English | MEDLINE | ID: mdl-39230938

ABSTRACT

Three Gram-stain-negative, aerobic, non-motile, chemoheterotrophic, short-rod-shaped bacteria, designated CDY1-MB1T, CDY2-MB3, and BDY3-MB2, were isolated from three marine sediment samples collected in the eastern Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains were related to the genus Aequorivita and close to the type strain of Aequorivita vitellina F4716T (with similarities of 98.0-98.1%). Strain CDY1-MB1T can grow at 15-37 °C (optimum 30 °C) and in media with pH 6-9 (optimum, pH 7), and tolerate up to 10% (w/v) NaCl. The predominant cellular fatty acids of strain CDY1-MB1T were iso-C15 : 0 (20.7%) and iso-C17 : 0 3-OH (12.8%); the sole respiratory quinone was menaquinone 6; the major polar lipids were phosphatidylethanolamine, two unidentified aminolipids and two unidentified polar lipids. The digital DNA-DNA hybridization/average nucleotide identity values between strains CDY1-MB1T, CDY2-MB3, and BDY3-MB2 and A. vitellina F4716T were 24.7%/81.6-81.7%, thereby indicating that strain CDY1-MB1T should represent a novel species of the genus Aequorivita. The genomic DNA G+C contents were 37.6 % in all three strains. Genomic analysis showed the presence of genes related to nitrogen and sulphur cycling, as well as metal reduction. The genetic traits of these strains indicate their possible roles in nutrient cycling and detoxification processes, potentially shaping the deep-sea ecosystem's health and resilience. Based upon the consensus of phenotypic and genotypic analyses, strain CDY1-MB1T should be classified as a novel species of the genus Aequorivita, for which the name Aequorivita flava sp. nov. is proposed. The type strain is CDY1-MB1T (=MCCC 1A16935T=KCTC 102223T).


Subject(s)
Bacterial Typing Techniques , Base Composition , DNA, Bacterial , Fatty Acids , Geologic Sediments , Nucleic Acid Hybridization , Phylogeny , RNA, Ribosomal, 16S , Seawater , Sequence Analysis, DNA , Vitamin K 2 , Geologic Sediments/microbiology , RNA, Ribosomal, 16S/genetics , Fatty Acids/chemistry , Pacific Ocean , Vitamin K 2/analogs & derivatives , Vitamin K 2/analysis , DNA, Bacterial/genetics , Seawater/microbiology , Phospholipids/analysis , Phosphatidylethanolamines , Flavobacteriaceae/isolation & purification , Flavobacteriaceae/genetics , Flavobacteriaceae/classification
17.
Water Sci Technol ; 89(2): 319-332, 2024 Jan.
Article in English | MEDLINE | ID: mdl-39219132

ABSTRACT

Marine fungi communities play a crucial role in the recycling of nutrients, restoration of biological systems, and the overall functioning of ecosystems. While aquatic fungal communities do react to pollution, there is a significant lack of information regarding the changes in the fungal community's structure, caused by marine pollution. In this study, we aim to address this gap in knowledge by investigating the range and makeup of fungal species present in marine environments in a polluted bay in Tunisia, spanning a biodiversity hotspot (Monastir Bay). Sequence analysis of the internal transcribed spacer region from culturable mycobiome and physicochemical parameters were investigated at seven sites in the bay. A total of 32 fungal taxa were identified at the genus and/or species levels and were assigned to four major groups (Aspergillacae 37.5%, Dothiomyceta 21.87%, Sordariamyceta 28.12%, and Yeasts 12.5%) with a remarkable predominance of Aspergillus genus. Assessment of the Shannon-Wiener diversity index and the Simpson dominance index revealed that the highest species diversity index (0.84) was recorded at the Kheniss site. Our results suggest the existence of diverse fungal communities, can be considered a useful community model for further ecological and evolutionary study of fungi in the bay.


Subject(s)
Bays , Biodiversity , Fungi , Tunisia , Fungi/genetics , Fungi/classification , Fungi/isolation & purification , Bays/microbiology , Mycobiome , Mediterranean Sea , Seawater/microbiology , Environmental Monitoring
18.
Science ; 385(6714): eaab2661, 2024 Sep 13.
Article in English | MEDLINE | ID: mdl-39265021

ABSTRACT

Lipids comprise a significant fraction of sinking organic matter in the ocean and play a crucial role in the carbon cycle. Despite this, our understanding of the processes that control lipid degradation is limited. We combined nanolipidomics and imaging to study the bacterial degradation of diverse algal lipid droplets and found that bacteria isolated from marine particles exhibited distinct dietary preferences, ranging from selective to promiscuous degraders. Dietary preference was associated with a distinct set of lipid degradation genes rather than with taxonomic origin. Using synthetic communities composed of isolates with distinct dietary preferences, we showed that lipid degradation is modulated by microbial interactions. A particle export model incorporating these dynamics indicates that metabolic specialization and community dynamics may influence lipid transport efficiency in the ocean's mesopelagic zone.


Subject(s)
Bacteria , Lipid Metabolism , Oceans and Seas , Phytoplankton , Bacteria/metabolism , Bacteria/genetics , Bacteria/classification , Lipid Droplets/metabolism , Microbial Interactions , Microbiota , Seawater/microbiology , Seawater/chemistry , Phytoplankton/metabolism
19.
Science ; 385(6714): 1167-1168, 2024 Sep 13.
Article in English | MEDLINE | ID: mdl-39265029

ABSTRACT

Marine bacteria cooperate to degrade lipids in sinking particulate organic matter.


Subject(s)
Aquatic Organisms , Bacteria , Lipid Metabolism , Seawater , Aquatic Organisms/metabolism , Bacteria/metabolism , Bacteria/genetics , Seawater/microbiology , Seawater/chemistry
20.
Geobiology ; 22(5): e12617, 2024.
Article in English | MEDLINE | ID: mdl-39295594

ABSTRACT

The increased difference in the sulfur isotopic compositions of sedimentary sulfate (carbonate-associated sulfate: CAS) and sulfide (chromium-reducible sulfur: CRS) during the Ediacaran Shuram excursion is attributed to increased oceanic sulfate concentration in association with the oxidation of the global ocean and atmosphere. However, recent studies on the isotopic composition of pyrites have revealed that CRS in sediments has diverse origins of pyrites. These pyrites are formed either in the water column/shallow sediments, where the system is open with respect to sulfate, or in deep sediments, where the system is closed with respect to sulfate. The δ34S value of sulfate in the open system is equal to that of seawater; on the contrary, the δ34S value of sulfate in the closed system is higher than that of seawater. Therefore, obtaining the isotopic composition of pyrites formed in an open system, which most likely retain microbial sulfur isotope fractionation, is essential to reconstruct the paleo-oceanic sulfur cycle. In this study, we carried out multiple sulfur isotope analyses of CRS and mechanically separated pyrite grains (>100 µm) using a fluorination method, in addition to secondary ion mass spectrometry (SIMS) analyses of in situ δ34S values of pyrite grains in drill core samples of Member 3 of the Ediacaran Doushantuo Formation in the Three Gorges area, South China. The isotope fractionation of microbial sulfate reduction (MSR) in the limestone layers of the upper part of Member 3 was calculated to be 34ε = 55.7‰ and 33λ = 0.5129 from the δ34S and Δ33S' values of medium-sized pyrite grains ranging from 100 to 300 µm and the average δ34S and Δ33S' values of CAS. Model calculations revealed that the influence of sulfur disproportionation on the δ34S values of these medium-sized pyrite grains was insignificant. In contrast, within the dolostone layers of the middle part of Member 3, isotope fractionation was determined to be 34ε = 47.5‰. The 34ε value in the middle part of Member 3 was calculated from the average δ34S values of the rim of medium-sized pyrite grains and the average δ34S values of CAS. This observation revealed an increase in microbial sulfur isotope fractionation during the Shuram excursion at the drill core site. Furthermore, our investigation revealed correlations between δ34SCRS values and CRS concentrations and between CRS and TOC concentrations, implying that organic matter load to sediments controlled the δ34SCRS values rather than oceanic sulfate concentrations. However, these CRS and TOC concentrations are local parameters that can change only at the kilometer scale with local redox conditions and the intensity of primary production. Therefore, the decreasing δ34SCRS values likely resulted from local redox conditions and not from a global increase in the oceanic sulfate concentration.


Subject(s)
Geologic Sediments , Sulfur Isotopes , Sulfur , Geologic Sediments/chemistry , Geologic Sediments/microbiology , China , Sulfur Isotopes/analysis , Sulfur/analysis , Sulfur/metabolism , Seawater/chemistry , Seawater/microbiology , Sulfides/analysis , Sulfides/metabolism , Sulfates/analysis , Sulfates/metabolism , Oceans and Seas , Iron
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