Bacterioplankton compositions of lakes and oceans: a first comparison based on fluorescence in situ hybridization

The Photoheterotroph Dokdonia sp. MED134 Modulates the Expression of Resource Acquisition and Anaplerotic Carbon Fixation Pathways in Response to Temperature

Temperature has an overriding impact on microbial physiology, but the molecular basis of thermal acclimation in many ecologically relevant marine bacterial taxa remains unexplored. We used quantitative transcriptomics to analyse the transcriptional reprogramming of a proteorhodopsin-based photoheterotroph, Dokdonia sp. MED134, during thermal acclimation from 10°C to 34°C. Temperature significantly impacted the expression of most MED134 genes (84%). Marker genes of the general stress response were induced towards cold temperature (10°C). Conversely, highly expressed genes associated with DNA replication and resource acquisition, like TonB-dependent transporters and gliding motility genes, were upregulated towards warm temperatures along this thermal range, when growth rates were fast. The mRNA transcript abundance of most genes related to the TCA cycle was not differentially expressed by temperature. By contrast, the expression of genes associated with anaplerotic carbon fixation was significantly enhanced at the optimum growth temperature (25°C). The expression of the proteorhodopsin was minimum at 10°C, and its regulation by light was impaired at 34°C, suggesting regulatory imbalances in this key phototrophic gene under supra-optimal warm conditions. Our findings highlight potential implications of growth temperature for regulating mechanisms of nutrient and energy acquisition, as well as the intracellular carbon flux in globally abundant marine photoheterotrophs.

A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential

With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.

Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster

BACKGROUND

The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.

RESULTS

The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.

CONCLUSIONS

Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.

Glacial meltwater and seasonality influence community composition of diazotrophs in Arctic coastal and open waters

The Arctic Ocean is particularly affected by climate change with unknown consequences for primary productivity. Diazotrophs-prokaryotes capable of converting atmospheric nitrogen to ammonia-have been detected in the often nitrogen-limited Arctic Ocean but distribution and community composition dynamics are largely unknown. We performed amplicon sequencing of the diazotroph marker gene nifH from glacial rivers, coastal, and open ocean regions and identified regionally distinct Arctic communities. Proteobacterial diazotrophs dominated all seasons, epi- to mesopelagic depths and rivers to open waters and, surprisingly, Cyanobacteria were only sporadically identified in coastal and freshwaters. The upstream environment of glacial rivers influenced diazotroph diversity, and in marine samples putative anaerobic sulphate-reducers showed seasonal succession with highest prevalence in summer to polar night. Betaproteobacteria (Burkholderiales, Nitrosomonadales, and Rhodocyclales) were typically found in rivers and freshwater-influenced waters, and Delta- (Desulfuromonadales, Desulfobacterales, and Desulfovibrionales) and Gammaproteobacteria in marine waters. The identified community composition dynamics, likely driven by runoff, inorganic nutrients, particulate organic carbon, and seasonality, imply diazotrophy a phenotype of ecological relevance with expected responsiveness to ongoing climate change. Our study largely expands baseline knowledge of Arctic diazotrophs-a prerequisite to understand underpinning of nitrogen fixation-and supports nitrogen fixation as a contributor of new nitrogen in the rapidly changing Arctic Ocean.

The compact genome of the sponge Oopsacas minuta (Hexactinellida) is lacking key metazoan core genes

BACKGROUND

Explaining the emergence of the hallmarks of bilaterians is a central focus of evolutionary developmental biology-evodevo-and evolutionary genomics. For this purpose, we must both expand and also refine our knowledge of non-bilaterian genomes, especially by studying early branching animals, in particular those in the metazoan phylum Porifera.

RESULTS

We present a comprehensive analysis of the first whole genome of a glass sponge, Oopsacas minuta, a member of the Hexactinellida. Studying this class of sponge is evolutionary relevant because it differs from the three other Porifera classes in terms of development, tissue organization, ecology, and physiology. Although O. minuta does not exhibit drastic body simplifications, its genome is among the smallest of animal genomes sequenced so far, and surprisingly lacks several metazoan core genes (including Wnt and several key transcription factors). Our study also provides the complete genome of a symbiotic Archaea dominating the associated microbial community: a new Thaumarchaeota species.

CONCLUSIONS

The genome of the glass sponge O. minuta differs from all other available sponge genomes by its compactness and smaller number of encoded proteins. The unexpected loss of numerous genes previously considered ancestral and pivotal for metazoan morphogenetic processes most likely reflects the peculiar syncytial tissue organization in this group. Our work further documents the importance of convergence during animal evolution, with multiple convergent evolution of septate-like junctions, electrical-signaling and multiciliated cells in metazoans.

Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment

BACKGROUND

Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear.

RESULTS

The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation.

CONCLUSION

This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.

Impacts of Seawater pH Buffering on the Larval Microbiome and Carry-Over Effects on Later-Life Disease Susceptibility in Pacific Oysters

Shellfish industries are threatened worldwide by recurrent summer mortality events. Such incidences are often associated with Vibrio disease outbreaks, and thus, it is critical that animals are able to mount sufficient immune responses.

Opportunistic diseases in marine eukaryotes: Could Bacteroidota be the next threat to ocean life?

Bacteria within the phylum Bacteroidota (Bacteroidetes) are known to cause devastating and widespread disease outbreaks in marine eukaryotic hosts. However, with few pathogens described in detail, their prevalence and virulence strategies remain largely unknown. Here, we systematically reviewed the literature to evaluate the current understanding of Bacteroidota that cause disease in marine hosts. Isolates affiliated with the genera Tenacibaculum and Aquimarina (Flavobacteriaceae) were the most widely reported and characterized pathogens. Although cultured isolates were predominantly Flavobacteriia, culture-independent studies also found classes Bacteroidia, Cytophagia and Sphingobacteriia associated with disease. We found that pathogenic marine Bacteroidota largely conformed to an opportunistic lifestyle but could also act as secondary pathogens or were involved in polymicrobial diseases. Many diseases were also associated with an environmental stressor, especially those affecting coral, macroalgae and fish. Key virulence traits included the production of adhesins and host tissue-degrading enzymes. Overall, the nature of disease involving Bacteroidota pathogens appears to be an outcome of complex host-pathogen-environment interactions; however, our understanding of virulence remains limited by the lack of functional characterization studies. This is concerning as Bacteroidota have the potential to emerge as a serious threat to marine ecosystems and aquaculture industries, driven by global changes in ocean conditions.

Field study on short-term changes in benthic environment and benthic microbial communities using pyrolyzed oyster shells

To evaluate the effect of pyrolyzed crushed oyster shells (PCOS) on the remediation of sediments and microbial diversity, a field study was conducted in Buksin Bay, Tongyeong City, Republic of Korea. It was observed that after treatment with PCOS, the concentration of H₂S in the sediment of the control site was 287 mg/L. Furthermore, it decreased up to 0 mg/L and remained so until the end of the field study, that is for a period of six months. Moreover, the concentrations of NO₂-N + NO₃-N, NH₄-N, and PO₄-P decreased sharply, and the oxidation-reduction potential (ORP) increased after PCOS treatment in pore water and overlying water. Regarding the diversity of microbial communities, the predominance of bacteria from phylum Chlorobi was observed in highly reduced (-410 mV; ORP) sediment, which is well known for the production of H₂S. After PCOS treatment, the relative abundance of Chlorobi was sharply suppressed. On the other hand, the predominance of bacteria from the phyla Proteobacteria and Bacteroidetes was observed, and their relative abundance in the PCOS-treated sediment increased throughout the experiment, based on 16S rRNA sequencing. The results demonstrate that the abundance of bacterial communities in the PCOS-treated sediments of Buksin Bay is important for marine ecological functioning, especially for pollutant transformation.

Gramella crocea sp. nov., isolated from activated sludge of a seafood processing plant

A novel aerobic Gram-negative strain, designated as YB25^T, was isolated from an activated sludge sample collected from a seafood processing plant in Zhoushan, Zhejiang Province, China, and characterized by using a polyphasic taxonomic approach in this study. Strain YB25^T was motile by gliding, and short-rod-shaped. The isolate grew at 4-37 °C (optimum 28 °C), pH 6.0-9.0 (optimum pH 7.0) and 0.0-10.0% NaCl (optimum 2.0%, w/v). Phylogenetic analysis based on 16S rRNA gene indicated that strain YB25^T belonged to the genus Gramella, and showed the highest sequence similarity of 97.59% to Gramella lutea YJ019^T. The DNA G + C content was 39.5%. In silico DNA-DNA hybridization (DDH) and average nucleotide identity (ANI) values between strain YB25^T with most closely strains were below the threshold, which is considered to the phylogenetic definition of a novel species. Chemotaxonomic analysis indicated that the only respiratory quinone was menaquinone-6 and the major fatty acids were iso-C_15:0, anteiso-C_15:0, iso-C_17:0 3-OH, and summed feature 9 (iso-C_17:1ω9c and C_16:0 10 methyl). The polar lipid profile was composed of phosphatidylethanolamine, an unidentified phospholipid, two unidentified amino lipids, three unidentified glycolipids, and four unidentified lipids. Compared with the reference strains, strain YB25^T contained higher abundance of genes for carbohydrates metabolism,nitrogen metabolism, sulfur metabolism and respiration based on its genomic metabolic pathways and had been found a certain potential in the degradation of pectin. On the basis of the taxonomic evidence, strain YB25^T represents a novel species of the genus Gramella, for which the name Gramella crocea sp. nov. is proposed. The type strain is YB25^T (= KCTC 82680 ^T = MCCC 1K05761^T).

Salinity as a Determinant Structuring Microbial Communities in Coastal Lakes

The response of bacterioplankton structure to salinity level in coastal lakes (n = 9) along the southern Baltic Sea coastline was studied. In terms of mean salinity levels (0.2−5.2 PSU), the lakes represented freshwater, transitional, and brackish types. Results showed that salinity determines the spatial and seasonal distribution patterns of microorganisms in costal lakes. Increased salinity contributed to a significant decline in total bacterial numbers (TBN). The TBN was lowest in brackish lakes in autumn (4 × 106 cells/mL) and highest in freshwater lakes in summer (7.11 × 106 cells/mL). The groups of Proteobacteria are appropriate bioindicators in any classifications of coastal ecosystems, particularly at low-haline stress. Alpha- and Gamma- subclasses of Proteobacteria are identifiers for brackish habitats, while Betaproteobacteria, due to their intolerance to haline stress, prefer freshwater habitats. Counts of euryhaline Actinobacteria, the dominant group of bacterioplankton (31.8%), decreased significantly with increased salinity. Actinobacteria and Deltaproteobacteria were identifiers of transitional lakes. Cytophaga-Flavobacteria showed affinity with freshwater ecosystems, but this relation was not statistically significant (p > 0.05). The bacteria groups correlated with other physico-chemical parameters of water, such as oxygenation (Actinobacteria) or organic carbon (Betaproteobacteria, Deltaproteobacteria). The impact of hydrological connectivity and salt-water interference on the microbiota structure and biogeochemistry of coastal waters should be considered in the assessment of the ecological status of coastal lakes.

A cautionary signal from the Red Sea on the impact of increased dust activity on marine microbiota

BACKGROUND

Global climate change together with growing desertification is leading to increased dust emissions to the atmosphere, drawing attention to possible impacts on marine ecosystems receiving dust deposition. Since microorganisms play important roles in maintaining marine homeostasis through nutrient cycling and carbon flow, detrimental changes in the composition of marine microbiota in response to increased dust input could negatively impact marine health, particularly so in seas located within the Global Dust Belt. Due to its strategic location between two deserts and unique characteristics, the Red Sea provides an attractive semi-enclosed "megacosm" to examine the impacts of large dust deposition on the vastly diverse microbiota in its exceptionally warm oligotrophic waters.

RESULTS

We used culture-independent metagenomic approaches to assess temporal changes in the Red Sea microbiota in response to two severe sandstorms, one originated in the Nubian Desert in the summer 2016 and a second one originated in the Libyan Desert in the spring 2017. Despite differences in sandstorm origin and meteorological conditions, both sandstorms shifted bacterial and Archaeal groups in a similar mode. In particular, the relative abundance of autotrophic bacteria declined while those of heterotrophic bacteria, particularly Bacteroidetes, and Archaea increased. The changes peaked within six days from the start of sandstorms, and the community recovered the original assemblage within one month.

CONCLUSION

Our results suggest that increased dust emission with expanding desertification could lead to undesirable impacts in ocean function, enhancing heterotrophic processes while reducing autotrophic ones, thereby affecting the marine food web in seas receiving dust deposition.

Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review

As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.

Contamination of antibiotics and sul and tet(M) genes in veterinary wastewater, river, and coastal sea in Thailand

Water systems in Southeast Asia accumulate antibiotics and antibiotic resistance genes (ARGs) from multiple origins, notably including human clinics and animal farms. To ascertain the fate of antibiotics and ARGs in natural water environments, we monitored the concentrations of these items in Thailand. Here, we show high concentrations of tetracyclines (72,156.9 ng/L) and lincomycin (23,968.0 ng/L) in pig farms, followed by nalidixic acid in city canals. The city canals and rivers contained diverse distributions of antibiotics and ARGs. Assessments of targeted ARGs, including sul1, sul2, sul3, and tet(M), showed that freshwater (pig farm wastewater, rivers, and canals) consistently contained these ARGs, but these genes were less abundant in seawater. Although sulfonamides were low concentrations (<170 ng/mL), sul1 and sul2 genes were abundant in freshwater (minimum 4.4 × 10^-3-maximum 1.0 × 10⁰ copies/16S), suggesting that sul genes have disseminated over a long period, despite cessation of use of this class of antibiotics. Ubiquitous distribution of sul genes in freshwater appeared to be independent of selection pressure. In contrast, water of the coastal sea in the monitored area was not contaminated by these antibiotics or ARGs. The density of Enterobacteriales was lower in seawater than in freshwater, suggesting that the number of ARG-possessing Enterobacteriales falls after entering seawater. From the pig farms, through rivers/canals, to the coastal sea, the occurrence of tetracyclines and tet(M) exhibited some correlation, although not a strong one. However, no correlations were found between concentrations of total antibiotics and ARGs, nor between sulfonamides and sul genes. This is the first comprehensive study showing Thai features of antibiotics and ARGs contaminations. The pig farm is hot spot of antibiotics and ARGs, and sul genes ubiquitously distribute in freshwater environments, which become less abundant in seawater.

Deltaproteobacterium Strain KaireiS1, a Mesophilic, Hydrogen-Oxidizing and Sulfate-Reducing Bacterium From an Inactive Deep-Sea Hydrothermal Chimney

A novel deltaproteobacterial, mesophilic, hydrogen-oxidizing, and sulfate-reducing bacterium (strain KaireiS1) was highly enriched from an inactive chimney located in the active zone of the Kairei hydrothermal vent field (Central Indian Ridge) in the Indian Ocean. Based on 16S rRNA gene analyses, strain KaireiS1 is the currently only cultured representative of a cluster of uncultured Deltaproteobacteria, positioned within the Desulfobulbaceae family, between the Desulfobulbus genus and the “Cable Bacteria.” A facultative autotrophic lifestyle of KaireiS1 is indicated by its growth in the absence of organic compounds, measurements of CO₂-fixation rates, and activity measurements of carbon monoxide dehydrogenase, the key enzyme of the reductive Acetyl-CoA pathway. Apart from hydrogen, strain KaireiS1 can also use propionate, lactate, and pentadecane as electron donors. However, the highest cell numbers were reached when grown autotrophically with molecular hydrogen. Hydrogen uptake activity was found in membrane and soluble fractions of cell-free extracts and reached up to 2,981±129 nmol H₂*min⁻¹*mg⁻¹ of partially purified protein. Commonly, autotrophic sulfate-reducing bacteria from the Deltaproteobacteria class, thriving in hydrothermal vent habitats are described as thermophiles. Given its physiological characteristics and specific isolation source, strain KaireiS1 demonstrates a previously unnoticed potential for microbial sulfate reduction by autotrophs taking place at moderate temperatures in hydrothermal vent fields.

Ice Melt-Induced Variations of Structural and Functional Traits of the Aquatic Microbial Community along an Arctic River (Pasvik River, Norway)

The effects of climate change-induced ice melting on the microbial communities in different glacial-fed aquatic systems have been reported, but seasonal dynamics remain poorly investigated. In this study, the structural and functional traits of the aquatic microbial community were assessed along with the hydrological and biogeochemical variation patterns of the Arctic Pasvik River under riverine and brackish conditions at the beginning (May = Ice-melt (−)) and during the ice-melting season (July = Ice-melt (+)). The microbial abundance and morphometric analysis showed a spatial diversification between the riverine and brackish stations. Results highlighted different levels of microbial respiration and activities with different carbon and phosphorous utilization pathways, thus suggesting an active biogeochemical cycling along the river especially at the beginning of the ice-melting period. At Ice-melt (−), Gammaproteobacteria and Alphaproteobacteria were dominant in riverine and brackish stations, respectively. Conversely, at Ice-melt (+), the microbial community composition was more homogeneously distributed along the river (Gammaproteobacteria > Alphaproteobacteria > Bacteroidetes). Our findings provide evidence on how riverine microbial communities adapt and respond to seasonal ice melting in glacial-fed aquatic ecosystems.

The Effect of Initial Conditions with Aerobic Biological Treatment on Aniline Dyeing Wastewater

According to the characteristics of aniline dyeing wastewater, aerobic biological treatment was adopted herein, and high-throughput sequencing technology was used to analyze the changes to the microbial community structure and diversity in the aerobic sludge acclimation stage. As a result, according to the experimental study on the effects of different biomass, the initial pH value and the salinity with the aerobic biological treatment, the chemical oxygen demand (COD) degradation rate can increase linearly with the increase in biomass under different biomass conditions. The organic matter degradation rate is 6.24 mg/L COD·h−1·(mg/L·MLSS)−1, with a correlation coefficient (R2) of 0.98704. When the initial pH value is less than 7.0 ± 0.2, the COD degradation rate increases with the increase in the initial pH value and then decreases gradually. The optimal sludge concentration is 4 g/L; the optimal initial pH value is in the range of 7.0–8.0; the optimal salinity is 1.7%. When the initial concentration of COD is 3000 mg/L, the COD value gradually stabilizes and decreases to 1500 mg/L after 32 h, the degradation rate reaches 50%, and the pH decreases from 7.5 to 4.5. Sphingopyxis has been detected in sludge samples from the third cycle of acclimation, which can biodegrade aromatic compounds, anthraquinone dyes, and their intermediates, and the relative abundance of Sphingopyxis increased from 0.18% to 5.08%, indicating a potential biodegradation ability of aniline dyeing wastewater.

Identification and analysis of the biological activity of the new strain of Pseudoalteromonas piscicida isolated from the hemal fluid of the bivalve Modiolus kurilensis (F. R. Bernard, 1983)

A cultivated form of bacteria (strain 2202) was isolated from the hemal fluid of the bivalve mollusk Modiolus kurilensis. Based on the set of data collected by genetic and physiological/biochemical analyses, the strain was identified as the species Pseudoalteromonas piscicida. Strain 2202 exhibits antimicrobial activity against Staphylococcus aureus, Candida albicans, and Bacillus subtilis but not against Escherichia coli and Pseudomonas aeruginosa. These activities characterize the behavior of strain 2202 as predator-like and classify it as a facultative predator. Being part of the normal microflora in the hemolymph of M. kurilensis, when external conditions change, strain 2202 shows features of opportunistic microflora. The strain 2202 exhibits selective toxicity towards larvae of various invertebrates: it impairs the early development of Mytilus edulis, but not of Strongylocentrotus nudus. Thus, the selective manner in which P. piscicida strains interact with various species of microorganisms and eukaryotes should be taken into consideration when using their biotechnological potential as a probiotic in aquaculture, source of antimicrobial substances, and factors that prevent fouling.

Effect of microorganisms on the fingerprint of the volatile compounds in pine nut (Pinus koraiensis) peptide powder during storage

Pine nut (Pinus koraiensis) peptide (PNP) powder possesses promising bioactivities. However, the powder may have the quality problem of becoming sticky and smelly. Therefore, the volatile compounds' fingerprint of PNP powder was established by headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). The essential spoilage microorganisms were confirmed by 16S rDNA amplicon sequencing. The antioxidant activity, which presents PNP powder's quality, decreased during storage with the highest value of (1.88 ± 0.18) × 10¹⁴ at day 30. Fifty-nine significantly changed signals were detected; eight compounds were considered as volatile marker compounds. Besides, Firmicutes and Cyanobacteria were the essential spoilage microorganisms in PNP powder at the phylum level. Significantly, unidentified_Chloroplast, which belongs to Cyanobacteria, had a positive correlation with volatile marker compounds. The results proved that microorganisms indeed affect volatile compounds of PNP powder and induced off-flavor, including hexanal, which can be used as the detection indicator for the quality control of PNP powder. PRACTICAL APPLICATIONS: In the present study, we controlled the influence of moisture migration on PNP powder and investigated microorganisms' effects on volatile compounds of PNP powder. HS-GC-IMS could be used to establish fingerprints of volatile compounds in PNP powder. 16S rDNA amplicon sequencing method could be used to screen the dominant spoilage bacteria in PNP powder and established essential spoilage microorganisms of PNP powder. This work provides a reference for category identification of PNP powder, which was infected by spoilage bacteria or not, and stored at day 0 or 30 days. Hexanal can be considered as the volatile marker compound generated from microorganisms. It helps to realize the controllability of PNP powder storage and prolongs the shelf life of PNP powder.

Description of Candidatus Mesopelagibacter carboxydoxydans and Candidatus Anoxipelagibacter denitrificans: Nitrate-reducing SAR11 genera that dominate mesopelagic and anoxic marine zones

The diverse and ubiquitous members of the SAR11 lineage (Alphaproteobacteria) represent up to 30-40% of the surface and mesopelagic oceanic microbial communities. However, the molecular and ecological mechanisms that differentiate closely related, yet distinct, SAR11 members that often co-occur under similar environmental conditions remain speculative. Recently, two mesopelagic and oxygen minimum zone (OMZ)-associated subclades of SAR11 (Ic and IIa.A) were described using single-cell amplified genomes (SAGs) linked to nitrate reduction in OMZs. In this current study, the collection of genomes belonging to these two subclades was expanded with thirteen new metagenome-assembled genomes (MAGs), thus providing a more detailed phylogenetic and functional characterization of these subclades. Gene content-based predictions of metabolic functions revealed similarities in central carbon metabolism between subclades Ic and IIa.A and surface SAR11 clades, with small variations in central pathways. These variations included more versatile sulfur assimilation pathways, as well as a previously predicted capacity for nitrate reduction that conferred unique versatility on mesopelagic-adapted clades compared to their surface counterparts. Finally, consistent with previously reported abundances of carbon monoxide (CO) in surface and mesopelagic waters, subclades Ia (surface) and Ic (mesopelagic) have the genetic potential to oxidize carbon monoxide (CO), presumably taking advantage of this abundant compound as an electron donor. Based on genomic analyses, environmental distribution and metabolic reconstruction, we propose two new SAR11 genera, Ca. Mesopelagibacter carboxydoxydans (subclade Ic) and Ca. Anoxipelagibacter denitrificans (subclade IIa.A), which represent members of the mesopelagic and OMZ-adapted SAR11 clades.

Experimentally-validated correlation analysis reveals new anaerobic methane oxidation partnerships with consortium-level heterogeneity in diazotrophy

Archaeal anaerobic methanotrophs ("ANME") and sulfate-reducing Deltaproteobacteria ("SRB") form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b-SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b-SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.

The Influence of the Addition of Plant-Based Natural Fibers (Jute) on Biocemented Sand Using MICP Method

The microbial-induced carbonate precipitation (MICP) method has gained intense attention in recent years as a safe and sustainable alternative for soil improvement and for use in construction materials. In this study, the effects of the addition of plant-based natural jute fibers to MICP-treated sand and the corresponding microstructures were measured to investigate their subsequent impacts on the MICP-treated biocemented sand. The fibers used were at 0%, 0.5%, 1.5%, 3%, 5%, 10%, and 20% by weight of the sand, while the fiber lengths were 5, 15, and 25 mm. The microbial interactions with the fibers, the CaCO₃ precipitation trend, and the biocemented specimen (microstructure) were also evaluated based on the unconfined compressive strength (UCS) values, scanning electron microscopy (SEM), and fluorescence microscopy. The results of this study showed that the added jute fibers improved the engineering properties (ductility, toughness, and brittleness behavior) of the biocemented sand using MICP method. Furthermore, the fiber content more significantly affected the engineering properties of the MICP-treated sand than the fiber length. In this study, the optimal fiber content was 3%, whereas the optimal fiber length was s 15 mm. The SEM results indicated that the fiber facilitated the MICP process by bridging the pores in the calcareous sand, reduced the brittleness of the treated samples, and increased the mechanical properties of the biocemented sand. The results of this study could significantly contribute to further improvement of fiber-reinforced biocemented sand in geotechnical engineering field applications.

Oligosaccharides derived from dragon fruit modulate gut microbiota, reduce oxidative stress and stimulate toll-pathway related gene expression in freshwater crustacean Daphnia magna

Dragon fruit oligosaccharide (DFO) is an indigestible prebiotic. In this study, we aimed to investigate the effects of DFO on gut microbiota, oxidative stress and immune-related gene expression in Daphnia magna. The 10-day-old D. magna were treated with 0, 9, and 27 mg l^-1 DFO for 85 h. The gut bacterial communities, superoxide dismutase (SOD) activity, lipid peroxidation and the expressions of genes in Toll signaling pathway were observed. The results showed that D. magna treated with 9 and 27 mg l^-1 DFO altered gut microbiota composition by increasing Limnohabitans and Lactobacillus, and significantly increased SOD activity and reduced lipid peroxidation. Moreover, the expressions of Toll2, Toll3, Toll5, Toll7 and Pelle genes were significantly increased in D. magna treated with 9 and 27 mg l^-1 DFO. Our results suggested that DFO changed the composition of the gut microbiota of D. magna by increasing the beneficial bacteria. DFO also had the ability to stimulate innate immunity in D. magna by increasing SOD activity, reducing lipid peroxidation, and increasing the expression of immune-related genes.

Microbiota composition of captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839)

The Labroides dimidiatus is one of the most traded marine ornamental fishes worldwide, yet not much is known about the microflora associated with this fish. This study is designed to investigate the bacteria composition associated with captive L. dimidiatus and its surrounding aquarium water. The fish and carriage water were obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Bacteria present on the skin and in the stomach and the aquarium water were enumerated using culture-independent approaches and next-generation sequencing (NGS) technology. A total of 3,238,564 valid reads and 828 total operational taxonomic units (OTUs) were obtained from the three metagenomic libraries using NGS analysis. Of all the 15 phyla identified in this study, Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were the most prevalent in all samples. Also, 170 families belonging to 36 bacteria classes were identified. Although many of the bacteria families were common in the skin, gut, and aquarium water (39%), about 26% of the families were exclusive to the aquarium water alone. Therefore, any substantial change in the structure and abundance of microbiota (especially pathogenic bacteria) reported in this study may serve as an early sign for disease infection in the species under captivity. KEY POINTS: • Proteobacteria was the most dominant. • The microbiota was either shared or exclusively in samples.

Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.

Microorganisms of Lake Baikal-the deepest and most ancient lake on Earth

Lake Baikal (Russia) is the largest (by volume) and deepest lake on Earth. The lake remains relatively pristine due to the low population density around its basin. Being very distant from any marine water body but having a remarkable number of similarities to oceans (depth, oxygen content, oligotrophy) provides a unique model of pelagic microbiota that is submitted to marine-like conditions minus the salt content of the water. It is also a model of lakes located at high latitudes and submitted to yearly ice cover (from January to April). The analysis by different approaches has indeed provided a view of the microbiota of this lake. It contains novel microbes that are closely related to marine groups not known to be present in freshwater like Chloroflexi or Pelagibacter. The deep water mass contains large communities of chemolithotrophs that use ammonia generated in the photic zone or methane from the sediments. KEY POINTS: • The chemical composition and limnic features of the deepest lake on Earth determine the vital activity of microorganisms. • The diversity, ecology, and role of individual taxa of microorganisms were studied using cultivation and molecular methods. • Data of large metagenomic datasets in the epipelagic and bathypelagic layers of the water column in southern Baikal were discussed.

In silico Prediction of Virus-Host Interactions for Marine Bacteroidetes With the Use of Metagenome-Assembled Genomes

Bacteroidetes is one of the most abundant heterotrophic bacterial taxa in the ocean and play crucial roles in recycling phytoplankton-derived organic matter. Viruses of Bacteroidetes are also expected to have an important role in the regulation of host communities. However, knowledge on marine Bacteroidetes viruses is biased toward cultured viruses from a few species, mainly fish pathogens or Bacteroidetes not abundant in marine environments. In this study, we investigated the recently reported 1,811 marine viral genomes to identify putative Bacteroidetes viruses using various in silico host prediction techniques. Notably, we used microbial metagenome-assembled genomes (MAGs) to augment the marine Bacteroidetes reference genomic data. The examined viral genomes and MAGs were derived from simultaneously collected samples. Using nucleotide sequence similarity-based host prediction methods, we detected 31 putative Bacteroidetes viral genomes. The MAG-based method substantially enhanced the predictions (26 viruses) when compared with the method that is solely based on the reference genomes from NCBI RefSeq (7 viruses). Previously unrecognized genus-level groups of Bacteroidetes viruses were detected only by the MAG-based method. We also developed a host prediction method based on the proportion of Bacteroidetes homologs in viral genomes, which detected 321 putative Bacteroidetes virus genomes including 81 that were newly recognized as Bacteroidetes virus genomes. The majority of putative Bacteroidetes viruses were detected based on the proportion of Bacteroidetes homologs in both RefSeq and MAGs; however, some were detected in only one of the two datasets. Putative Bacteroidetes virus lineages included not only relatives of known viruses but also those phylogenetically distant from the cultured viruses, such as marine Far-T4 like viruses known to be widespread in aquatic environments. Our MAG and protein homology-based host prediction approaches enhanced the existing knowledge on the diversity of Bacteroidetes viruses and their potential interaction with their hosts in marine environments.

Prokaryotic Diversity and Composition of Sediments From Prydz Bay, the Antarctic Peninsula Region, and the Ross Sea, Southern Ocean

The V3–V4 hypervariable regions of the 16S ribosomal RNA gene were analyzed to assess prokaryotic diversity and community compositions within 19 surface sediment samples collected from three different regions (depth: 250–3,548 m) of Prydz Bay, the Antarctic Peninsula region, and the Ross Sea. In our results, we characterized 1,079,709 clean tag sequences representing 43,227 operational taxonomic units (OTUs, 97% similarity). The prokaryotic community distribution exhibited obvious geographical differences, and the sequences formed three distinct clusters according to the samples’ origins. In general, the biodiversity of Prydz Bay was higher than those of the Antarctic Peninsula region and the Ross Sea, and there were similar prokaryotic communities in different geographic locations. The most dominant clades in the prokaryotic communities were Proteobacteria, Bacteroidetes, Thaumarchaeota, Oxyphotobacteria, Deinococcus-Thermus, Firmicutes, Acidobacteria, Fusobacteria, and Planctomycetes, but unique prokaryotic community compositions were found in each of the sampling regions. Our results also demonstrated that the prokaryotic diversity and community distribution were mainly influenced by geographical and physicochemical factors, such as Zn, V, Na, K, water depth, and especially geographical distance (longitude variation of sample location) and Ba ion content. Moreover, geochemical factors such as nutrient contents (TC, P, and Ca) also played important roles in prokaryotic diversity and community distribution. This represents the first report that Ba ion content has an obvious effect on prokaryotic diversity and community distribution in Southern Ocean sediments.

Groundwater microbial diversity and antibiotic resistance linked to human population density in Yucatan Peninsula, Mexico

Microbial community composition in selected karst groundwater sites in the Yucatan Peninsula, Mexico, was assessed to determine the environmental variables influencing groundwater microbial diversity. The karst aquifer system is a groundwater-dependent ecosystem and is the world’s second largest underwater karst cave system. The area’s geology allows precipitation to infiltrate into the groundwater system and prevents accumulation of surface water; as such, groundwater is the only source of fresh water on the peninsula. The sampling locations consisted of three karst sinkholes that extend through the freshwater zone into the saline water, and an abandoned drinking water well of an ocean-side resort, during the dry and rainy seasons. The analysis showed that highly diverse microbial communities are present in the Yucatan groundwater, sustained by permanently warm temperatures and high nutrient input from human activity. Proximity to densely populated areas, such as tourist resorts, is the most important factor influencing both the diversity and presence of fecal bacteria and the antibiotic resistance profile.

Distinctive tasks of different cyanobacteria and associated bacteria in carbon as well as nitrogen fixation and cycling in a late stage Baltic Sea bloom

Cyanobacteria and associated heterotrophic bacteria hold key roles in carbon as well as nitrogen fixation and cycling in the Baltic Sea due to massive cyanobacterial blooms each summer. The species specific activities of different cyanobacterial species as well as the N- and C-exchange of associated heterotrophic bacteria in these processes, however, are widely unknown. Within one time series experiment we tested the cycling in a natural, late stage cyanobacterial bloom by adding 13C bi-carbonate and 15N2, and performed sampling after 10 min, 30 min, 1 h, 6 h and 24 h in order to determine the fixing species as well as the fate of the fixed carbon and nitrogen in the associations. Uptake of 15N and 13C isotopes by the most abundant cyanobacterial species as well as the most abundant associated heterotrophic bacterial groups was then analysed by NanoSIMS. Overall, the filamentous, heterocystous species Dolichospermum sp., Nodularia sp., and Aphanizomenon sp. revealed no or erratic uptake of carbon and nitrogen, indicating mostly inactive cells. In contrary, non-heterocystous Pseudanabaena sp. dominated the nitrogen and carbon fixation, with uptake rates up to 1.49 ± 0.47 nmol N h-1 l-1 and 2.55 ± 0.91 nmol C h-1 l-1. Associated heterotrophic bacteria dominated the subsequent nitrogen remineralization with uptake rates up to 1.2 ± 1.93 fmol N h-1 cell -1, but were also indicative for fixation of di-nitrogen.

Integrating Hydrogeological and Microbiological Data and Modelling to Characterize the Hydraulic Features and Behaviour of Coastal Carbonate Aquifers: A Case in Western Cuba

Carbonate aquifers are the primary source of freshwater in Cuba. Unfortunately, coastal groundwater is often contaminated by seawater intrusion. The main aim of the present study was to test the efficacy of an experimental modelling approach, ranging from hydrogeology/geomorphology to microbiology, to better characterise both the hydraulic features and behaviour of a coastal carbonate aquifer and acquire useful information to prevent groundwater salinization. The interdisciplinary approach was an effective tool in order to understand (i) the hydraulic role played by some fault zones; (ii) the influence of discontinuous heterogeneities on groundwater flow and saltwater wedge shape; (iii) mixing processes between different water bodies (groundwater, surface water, seawater); (iv) the role of karst conduits in influencing the step-like halocline within the mixing zone between fresh groundwater and seawater.

Isolation and polyphasic identification of Tateyamaria armeniaca sp. nov

A novel alphaproteobacterium, designated KMU-156T, was isolated from seawater collected on the coast of Jeju Island, Republic of Korea, and its phylogenetic position was determined using a polyphasic taxonomic approach. Strain KMU-156T was Gram-stain-negative, strictly aerobic, apricot-colored, rod-shaped, non-motile and chemoorganoheterotrophic. Phylogenetic study based on the 16S rRNA gene sequence revealed that the novel bacterium belongs to the family ‘Rhodobacteraceae’, of the class Alphaproteobacteria, and that it possessed the greatest sequence similarity (98.2%) with Tateyamaria omphalii MKT107T. DNA–DNA hybridization values between strains KMU-156T, T. omphalii KCTC 12333T and Tateyamaria pelophila DSM 17270T were less than 70%. The major isoprenoid quinone of the novel isolate was ubiquinone-10 (Q-10) and the major (> 10%) cellular fatty acids were C16:0 and C18:1 ω7c. The genomic DNA G + C content of strain KMU-156T was 59.3 mol%. The polar lipid profile of the strain KMU-156T had phosphatidylglycerol, phosphatidylcholine, an unidentified aminolipid, an unidentified phospholipid and two unidentified lipids. From the discriminative taxonomic features, the strain is considered to represent a novel species of the genus Tateyamaria for which the name Tateyamaria armeniaca sp. nov. is proposed. The type strain of T. armeniaca sp. nov. is KMU-156T (= KCCM 90321T = NBRC 113460T).

Bulbiferates A and B: Antibacterial Acetamidohydroxybenzoates from a Marine Proteobacterium, Microbulbifer sp

Here we report the discovery of two new 3-acetamido-4-hydroxybenzoate esters, bulbiferates A (1) and B (2), isolated from Microbulbifer sp. cultivated from the marine tunicate Ecteinascidia turbinata. The structures of 1 and 2 were determined by analysis of 2D NMR and MS data. Additionally, three synthetic analogues (3-5), differing in ester sizes/lengths, were prepared for the purposes of evaluating potential structure-activity relationships; no clear correlations tying ester lengths to activity were evident. Bulbiferates A (1) and B (2) demonstrated antibacterial activity against both Escherichia coli (E. coli) and methicillin-sensitive Staphylococcus aureus (MSSA), whereas the synthetic analogues 3 and 4 displayed activity only against MSSA.

Microbial transformation of virus-induced dissolved organic matter from picocyanobacteria: coupling of bacterial diversity and DOM chemodiversity

Picocyanobacteria make up half of the ocean's primary production, and they are subjected to frequent viral infection. Viral lysis of picocyanobacteria is a major driving force converting biologically fixed carbon into dissolved organic carbon (DOC). Viral-induced dissolved organic matter (vDOM) released from picocyanobacteria provides complex organic matter to bacterioplankton in the marine ecosystem. In order to understand how picocyanobacterial vDOM are transformed by bacteria and the impact of this process on bacterial community structure, viral lysate of picocyanobacteria was incubated with coastal seawater for 90 days. The transformation of vDOM was analyzed by ultrahigh-resolution mass spectrometry and the shift of bacterial populations analyzed using high-throughput sequencing technology. Addition of picocyanobacterial vDOM introduced abundant nitrogen components into the coastal water, which were largely degraded during the 90 days' incubation period. However, some DOM signatures were accumulated and the total assigned formulae number increased over time. In contrast to the control (no addition of vDOM), bacterial community enriched with vDOM changed markedly with increased biodiversity indices. The network analysis showed that key bacterial species formed complex relationship with vDOM components, suggesting the potential correspondence between bacterial populations and DOM molecules. We demonstrate that coastal bacterioplankton are able to quickly utilize and transform lysis products of picocyanobacteria, meanwhile, bacterial community varies with changing chemodiverisity of DOM. vDOM released from picocyanobacteria generated a complex labile DOM pool, which was converted to a rather stable DOM pool after microbial processing in the time frame of days to weeks.

Occurrence of sul and tet(M) genes in bacterial community in Japanese marine aquaculture environment throughout the year: Profile comparison with Taiwanese and Finnish aquaculture waters

The use of antibiotics in aquaculture causes selection pressure for antibiotic-resistant bacteria (ARB). Antibiotic resistance genes (ARGs) may persist in ARB and the environment for long time even after stopping drug administration. Here we show monthly differences in the occurrences of genes conferring resistance to sulfonamides (i.e. sul1, sul2, sul3), and tetracyclines (tet(M)) in Japanese aquaculture seawater accompanied by records of drug administration. sul2 was found to persist throughout the year, whereas the occurrences of sul1, sul3, and tet(M) changed month-to-month. sul3 and tet(M) were detected in natural bacterial assemblages in May and July, but not in colony-forming bacteria, thus suggesting that the sul3 was harbored by the non-culturable fraction of the bacterial community. Comparison of results from Taiwanese, Japanese, and Finnish aquaculture waters reveals that the profile of sul genes and tet(M) in Taiwan resembles that in Japan, but is distinct from that in Finland. To our knowledge, this work represents the first report to use the same method to compare the dynamics of sul genes and tet(M) in aquaculture seawater in different countries.

Ecogenomic characterization of widespread, closely-related SAR11 clades of the freshwater genus "Candidatus Fonsibacter" and proposal of Ca. Fonsibacter lacus sp. nov

The ubiquitous alpha-proteobacteria of the order "Candidatus Pelagibacterales" (SAR11) are highly abundant in aquatic environments, and among them, members of the monophyletic lineage LD12 (also known as SAR11 clade IIIb) are specifically found in lacustrine ecosystems. Clade IIIb bacteria are some of the most prominent members of freshwater environments, but little is known about their biology due to the lack of genome representatives. Only recently, the first non-marine isolate was cultured and described as "Candidatus Fonsibacter ubiquis". Here, we expand the collection of freshwater IIIb representatives and describe a new IIIb species of the genus "Ca. Fonsibacter". Specifically, we assembled a collection of 67 freshwater metagenomic datasets from the interconnected lakes of the Chattahoochee River basin (GA, USA) and obtained nearly complete metagenome-assembled genomes (MAGs) representing 5 distinct IIIb subclades, roughly equivalent to species based on genomic standards, including the previously described "Ca. F. ubiquis". Genomic comparisons between members of the IIIb species revealed high similarity in gene content. However, when comparing their abundance profiles in the Chattahoochee basin and various aquatic environments, differences in temporal and spatial distributions among the distinct species were observed implying niche differentiation might be underlying the coexistence of the highly functionally similar representatives. The name Ca. Fonsibacter lacus sp. nov. is proposed for the most abundant and widespread species in the Chattahoochee River basin and various freshwater ecosystems.

Microcapillary sampling of Baltic Sea copepod gut microbiomes indicates high variability among individuals and the potential for methane production

The paradox of methane oversaturation in oxygenated surface water has been described in many pelagic systems and still raises the question of the source. Temora sp. and Acartia sp. commonly dominate the surface and subsurface waters of the central Baltic Sea. It is hypothesised that their gut microbiome at least partly contributes to the methane anomaly in this ecosystem. However, the potential pathway for this methane production remains unclear. Using a microcapillary technique, we successfully overcame the challenge of sampling the gut microbiome of copepods <1 mm. 16S rRNA gene amplicon sequencing revealed differences among the dominant bacterial communities associated with Temora sp. (Actinobacteria, Betaproteobacteria and Flavobacteriia) and Acartia sp. (Actinobacteria, Alphaproteobacteria and Betaproteobacteria) and the surrounding water (Proteobacteria, Cyanobacteria and Verrucomicrobia), but also intraspecific variability. In both copepods, gut-specific prokaryotic taxa and indicative species for methane production pathways (methanogenesis, dimethylsulfoniopropionate or methylphosphonate) were present. The relative abundance of archaea and methanogens was investigated using droplet digital polymerase chain reaction and showed a high variability among copepod individuals, underlining intra- and interspecific differences in copepod-associated prokaryotic communities. Overall, this work highlights that the guts of Temora sp. and Acartia sp. have the potential for methane production but are probably no hotspot.

Bacterial diversity in the water column of meromictic Lake Cadagno and evidence for seasonal dynamics

The meromictic Lake Cadagno is characterized by a compact chemocline with high concentrations of anoxygenic phototrophic purple and green sulfur bacteria. However, a complete picture of the bacterial diversity, and in particular of effects of seasonality and compartmentalization is missing. To characterize bacterial communities and elucidate relationships between them and their surrounding environment high-throughput 16S rRNA gene pyrosequencing was conducted. Proteobacteria, Chlorobi, Verrucomicrobia, and Actinobacteria were the dominant groups in Lake Cadagno water column. Moreover, bacterial interaction within the chemocline and between oxic and anoxic lake compartments were investigated through fluorescence in situ hybridization (FISH) and flow cytometry (FCM). The different populations of purple sulfur bacteria (PSB) and green sulfur bacteria (GSB) in the chemocline indicate seasonal dynamics of phototrophic sulfur bacteria composition. Interestingly, an exceptional bloom of a cyanobacteria population in the oxic-anoxic transition zone affected the common spatial distribution of phototrophic sulfur bacteria with consequence on chemocline location and water column stability. Our study suggests that both bacterial interactions between different lake compartments and within the chemocline can be a dynamic process influencing the stratification structure of Lake Cadagno water column.

Diversity and seasonal distribution of ammonia-oxidizing archaea in the water column of a tropical estuary along the southeast Arabian Sea

Diversity and distribution pattern of ammonia-oxidizing archaea (AOA) were studied across a salinity gradient in the water column of Cochin Estuary (CE), a tropical monsoonal estuary along the southeast Arabian Sea. The water column of CE was found to be nutrient rich with high bacterial (3.7-6.7 × 10⁸ cells L^-1) and archaeal abundance (1.9-4.5 × 10⁸ cells L^-1). Diversity and seasonal variation in the distribution pattern of AOA were studied using clone library analysis and Denaturing gradient gel electrophoresis (DGGE). Clone library analysis of both the amoA and 16S rRNA gene sequences showed similar diversity pattern, however the diversity was more clear when the 16S rRNA gene sequences were analyzed. More than 70% of the sequences retrieved were clustered under uncultured Thaumarchaeota group 1 lineage and the major fractions of the remaining sequences were grouped into the Nitrosopumilus lineage and Nitrosopelagicus lineage. The AOA community in the CE was less adaptable to changing environmental conditions and its distribution showed seasonal variations within the DGGE banding pattern with higher diversity during the pre-monsoon period. The distribution of AOA also showed its preference to intermediate salinity for their higher diversity. Summer monsoon associated runoff and flushing played a critical role in regulating the seasonality of AOA distribution.

Characterization of microbes and denitrifiers attached to two species of floating plants in the wetlands of Lake Taihu

Biofilms are often observed at the solid-water interface. The leaves of many floating macrophytes have characteristics of both terrestrial plants and submerged macrophytes, because, in general, their upper and lower surfaces are exposed to air and water, respectively. However, little is known about the biofilms attached to floating plants. We investigated biofilms attached to the leaves, stems and roots of the floating plants Nymphoides peltata (in summer and winter) and Trapa natans (in summer) in the Gonghu Bay of Lake Taihu. Bacteria and algae were major components of the biofilm on the leaves of the two species of plants. In addition, 454 pyrosequencing analysis of bacterial 16S rRNA genes revealed that Proteobacteria was the dominant phylum, followed by Bacteroidetes, Firmicutes, Chloroflexi, Acidobacteria, and Verrucomicrobia. Cluster analysis showed that bacterial communities from the same plant source were clustered into the same group. A total of 677 genera were detected, and 47 genera were shared by all samples. Nitrifiers, including Nitrosomonas, Nitrosococcus and Nitrospira were detected in this study. Seven denitrifying genes (napA, napG, nirS, nirK, cnorB, qnorB and nosZ) were used to detect the abundance of denitrifiers. Genes nirK, nirS cnorB and nosZ were the four most abundant genes in all samples. Our results demonstrated that cultivation of floating plants in water column could enlarge the area for biofilm growth, and biofilms might play an important role in denitrification in eutrophic water.

Microbial communities in the nepheloid layers and hypoxic zones of the Canary Current upwelling system

Eastern boundary upwelling systems (EBUSs) are among the most productive marine environments in the world. The Canary Current upwelling system off the coast of Mauritania and Morocco is the second most productive of the four EBUS, where nutrient‐rich waters fuel perennial phytoplankton blooms, evident by high chlorophyll a concentrations off Cape Blanc, Mauritania. High primary production leads to eutrophic waters in the surface layers, whereas sinking phytoplankton debris and horizontally dispersed particles form nepheloid layers (NLs) and hypoxic waters at depth. We used Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD‐FISH) in combination with fatty acid (measured as methyl ester; FAME) profiles to investigate the bacterial and archaeal community composition along transects from neritic to pelagic waters within the “giant Cape Blanc filament” in two consecutive years (2010 and 2011), and to evaluate the usage of FAME data for microbial community studies. We also report the first fatty acid profile of Pelagibacterales strain HTCC7211 which was used as a reference profile for the SAR11 clade. Unexpectedly, the reference profile contained low concentrations of long chain fatty acids 18:1 cis11, 18:1 cis11 11methyl, and 19:0 cyclo11–12 fatty acids, the main compounds in other Alphaproteobacteria. Members of the free‐living SAR11 clade were found at increased relative abundance in the hypoxic waters in both years. In contrast, the depth profiles of Gammaproteobacteria (including Alteromonas and Pseudoalteromonas), Bacteroidetes, Roseobacter, and Synechococcus showed high abundances of these groups in layers where particle abundance was high, suggesting that particle attachment or association is an important mechanisms of dispersal for these groups. Collectively, our results highlight the influence of NLs, horizontal particle transport, and low oxygen on the structure and dispersal of microbial communities in upwelling systems.

Exploring biogeographic patterns of bacterioplankton communities across global estuaries

Estuaries provide an ideal niche to study structure and function of bacterioplankton communities owing to the presence of a multitude of environmental stressors. Bacterioplankton community structures from nine global estuaries were compared to understand their broad‐scale biogeographic patterns. Bacterioplankton community structure from four estuaries of Sundarbans, namely Mooriganga, Thakuran, Matla, and Harinbhanga, was elucidated using Illumina sequencing. Bacterioplankton communities from these estuaries were compared against available bacterioplankton sequence data from Columbia, Delaware, Jiulong, Pearl, and Hangzhou estuaries. All nine estuaries were dominated by Proteobacteria. Other abundant phyla included Bacteroidetes, Firmicutes, Acidobacteria, Actinobacteria, Cyanobacteria, Planctomycetes, and Verrucomicrobia. The abundant bacterial phyla showed a ubiquitous presence across the estuaries. At class level, the overwhelming abundance of Gammaproteobacteria in the estuaries of Sundarbans and Columbia estuary clearly stood out amidst high abundance of Alphaproteobacteria observed in the other estuaries. Abundant bacterial families including Rhodobacteriaceae, Shingomonadaceae, Acidobacteriaceae, Vibrionaceae, and Xanthomondaceae also showed ubiquitous presence in the studied estuaries. However, rare taxa including Chloroflexi, Tenericutes, Nitrospirae, and Deinococcus‐Thermus showed clear site‐specific distribution patterns. Such distribution patterns were also reinstated by nMDS ordination plots. Such clustering patterns could hint toward the potential role of environmental parameters and substrate specificity which could result in distinct bacterioplankton communities at specific sites. The ubiquitous presence of abundant bacterioplankton groups along with their strong correlation with surface water temperature and dissolved nutrient concentrations indicates the role of such environmental parameters in shaping bacterioplankton community structure in estuaries. Overall, studies on biogeographic patters of bacterioplankton communities can provide interesting insights into ecosystem functioning and health of global estuaries.

Environmental and hydroclimatic factors influencing Vibrio populations in the estuarine zone of the Bengal delta

The objective of this study was to determine environmental parameters driving Vibrio populations in the estuarine zone of the Bengal delta. Spatio-temporal data were collected at river estuary, mangrove, beach, pond, and canal sites. Effects of salinity, tidal amplitude, and a cyclone and tsunami were included in the study. Vibrio population shifts were found to be correlated with tide-driven salinity and suspended particulate matter (SPM). Increased abundance of Vibrio spp. in surface water was observed after a cyclone, attributed to re-suspension of benthic particulate organic carbon (POC), and increased availability of chitin and dissolved organic carbon (DOC). Approximately a two log₁₀ increase in the (p < 0.05) number of Vibrio spp. was observed in < 20 μm particulates, compared with microphytoplankton (20-60 μm) and zooplankton > 60 μm fractions. Benthic and suspended sediment comprised a major reservoir of Vibrio spp. Results of microcosm experiments showed enhanced growth of vibrios was related to concentration of organic matter in SPM. It is concluded that SPM, POC, chitin, and salinity significantly influence abundance and distribution of vibrios in the Bengal delta estuarine zone.

Contrasting Network Features between Free-Living and Particle-Attached Bacterial Communities in Taihu Lake

Free-living (FL) and particle-attached (PA) bacterial communities play critical roles in nutrient cycles, metabolite production, and as a food source in aquatic systems, and while their community composition, diversity, and functions have been well studied, we know little about their community interactions, co-occurrence patterns, and niche occupancy. In the present study, 13 sites in Taihu Lake were selected to study the differences of co-occurrence patterns and niches occupied between the FL and PA bacterial communities using correlation-based network analysis. The results show that both FL and PA bacterial community networks were non-random and significant differences of the network indexes (average path length, clustering coefficient, modularity) were found between the two groups. Furthermore, the PA bacterial community network consisted of more correlations between fewer OTUs, as well as higher average degree, making it more complex. The results of observed (O) to random (R) ratios of intra- or inter-phyla connections indicate more relationships such as cross-feeding, syntrophic, mutualistic, or competitive relationships in the PA bacterial community network. We also found that four OTUs (OTU00074, OTU00755, OTU00079, and OTU00454), which all had important influences on the nutrients cyclings, played different roles in the two networks as connectors or module hubs. Analysis of the relationships between the module eigengenes and environmental variables demonstrated that bacterial groups of the two networks favored quite different environmental conditions. These findings further confirmed the different ecological functions and niches occupied by the FL and PA bacterial communities in the aquatic ecosystem.

Bacterial community structure analysis of a hot spring soil by next generation sequencing of ribosomal RNA

In the present study the whole bacterial community structure of Tapovan hot spring soil located in the state of Uttarakhand, India was analysed through next generation sequencing. The hot spring soil is slightly alkaline in nature with abundance of sulphur. The spring soil was rich in various metallic and non-metallic elements required for bacterial survival. The community was found to comprise of 14 bacterial phyla with representation of members belonging to Firmicutes, Proteobacteria, Thermi, Bacteroidetes, Aquificae, Actinobacteria, chloroflexi, TM7, Fusobacteria etc. At the genus level Bacillus, Pseudomonas, Symbiobacterium, Thermus, Geobacillus, Anoxybacillus were found in abundance as compared to other genera like Flavobacterium, Ureibacillus, Clostridium, Meiothermus, Acinetobacter, Desulfotomaculum and Rheinheimera.

Spongiibacterium fuscum sp. nov., a marine Flavobacteriaceae isolated from the hard coral Galaxea fascicularis

A novel marine bacterium, designated 04OKA-3-218^T, was isolated from the hard coral Galaxea fascicularis L. collected in Japan. The strain was dark-brown-pigmented, Gram-negative, strictly aerobic, curved-rod-shaped and non-motile. Phylogenetic analysis based on the 16S rRNA gene sequence showed the affiliation of the isolate with members of the family Flavobacteriaceae of the phylum Bacteroidetes, with the highest sequence similarity (95.2%) to Spongiibacterium pacificum SW169^T. The DNA G+C content was 42.9 mol%; MK-6 was the major menaquinone; with iso-C17:0 3-OH (28.8%), iso-C15:0 (26.8%) and iso-C15:1 H and/or C13:0 3-OH (21.2%) as the main (>  10%) cellular fatty acids. The major polar lipid profile consisted of phosphatidylethanolamine, two unidentified aminolipids, two unidentified phosphoaminolipids and three unidentified lipids. On the basis of distinct phylogenetic and phenotypic evidences, the strain represents a novel species of the genus Spongiibacterium, for which the name Spongiibacterium fuscum sp. nov. is proposed. The type strain of S. fuscum sp. nov. is 04OKA-3-218^T (= KCTC 62504^T = NBRC 113248^T).

Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy

Phylogenetically diverse environmental ANME archaea and sulfate-reducing bacteria cooperatively catalyze the anaerobic oxidation of methane oxidation (AOM) in multicelled consortia within methane seep environments. To better understand these cells and their symbiotic associations, we applied a suite of electron microscopy approaches, including correlative fluorescence in situ hybridization-electron microscopy (FISH-EM), transmission electron microscopy (TEM), and serial block face scanning electron microscopy (SBEM) three-dimensional (3D) reconstructions. FISH-EM of methane seep-derived consortia revealed phylogenetic variability in terms of cell morphology, ultrastructure, and storage granules. Representatives of the ANME-2b clade, but not other ANME-2 groups, contained polyphosphate-like granules, while some bacteria associated with ANME-2a/2c contained two distinct phases of iron mineral chains resembling magnetosomes. 3D segmentation of two ANME-2 consortium types revealed cellular volumes of ANME and their symbiotic partners that were larger than previous estimates based on light microscopy. Polyphosphate-like granule-containing ANME (tentatively termed ANME-2b) were larger than both ANME with no granules and partner bacteria. This cell type was observed with up to 4 granules per cell, and the volume of the cell was larger in proportion to the number of granules inside it, but the percentage of the cell occupied by these granules did not vary with granule number. These results illuminate distinctions between ANME-2 archaeal lineages and partnering bacterial populations that are apparently unified in their ability to perform anaerobic methane oxidation.IMPORTANCE Methane oxidation in anaerobic environments can be accomplished by a number of archaeal groups, some of which live in syntrophic relationships with bacteria in structured consortia. Little is known of the distinguishing characteristics of these groups. Here, we applied imaging approaches to better understand the properties of these cells. We found unexpected morphological, structural, and volume variability of these uncultured groups by correlating fluorescence labeling of cells with electron microscopy observables.

Efficiency in hydrocarbon degradation and biosurfactant production by Joostella sp. A8 when grown in pure culture and consortia

Joostella strains are emerging candidates for biosurfactant production. Here such ability was analyzed for Joostella strain A8 in comparison with Alcanivorax strain A53 and Pseudomonas strain A6, all previously isolated from hydrocarbon enrichment cultures made of polychaete homogenates. In pure cultures Joostella sp. A8 showed the highest stable emulsion percentage (78.33%), hydrophobicity rate (62.67%), and an optimal surface tension reduction during growth in mineral medium supplemented with diesel oil (reduction of about 12mN/m), thus proving to be highly competitive with Alcanivorax and Pseudomonas strains. During growth in pure culture different level of biodegradation were detected for Alcanivorax strain A53 (52.7%), Pseudomonas strain A6 (38.2%) and Joostella strain A8 (26.8%). When growing in consortia, isolates achieved similar abundance values, with the best efficiency that was observed for the Joostella-Pseudomonas co-culture. Gas-chromatographic analysis revealed an increase in the biodegradation efficiency in co-cultures (about 90%), suggesting that the contemporary action of different bacterial species could improve the process. Results were useful to compare the efficiencies of well-known biosurfactant producers (i.e. Pseudomonas and Alcanivorax representatives) with a still unknown biosurfactant producer, i.e. Joostella, and to confirm them as optimal biosurfactant-producing candidates.