Planktonic and early-stage biofilm microbiota respond contrastingly to thermal discharge-created seawater warming.

Thermal-discharges from power plants highly disturb the biological communities of the receiving water body and understanding their influence is critical, given the relevance to global warming. We employed 16 S rRNA gene sequencing to examine the response of two dominant marine bacterial lifestyles (planktonic and biofilm) against elevated seawater temperature (+5 â„ƒ). Obtained results demonstrated that warming prompted high heterogeneity in diversity and composition of planktonic and biofilm microbiota, albeit both communities responded contrastingly. Alpha diversity revealed that temperature exhibited positive effect on biofilm microbiota and negative effect on planktonic microbiota. The community composition of planktonic microbiota shifted significantly in warming area, with decreased abundances of Bacteroidetes, Cyanobacteria, and Actinobacteria. Contrastingly, these bacterial groups exhibited opposite trend in biofilm microbiota. Co-occurrence networks of biofilm microbiota displayed higher node diversity and co-presence in warming area. The study concludes that with increasing ocean warming, marine biofilms and biofouling management strategies will be more challenging.

Exploring the impacts of heavy metals on spatial variations of sediment-associated bacterial communities.

One of the fundamental objectives in modern ecology is to decipher how bacterial communities in natural environment respond to anthropogenic activities. In recent times consequences of marine pollution, especially with heavy metals (HMs) have received increasing attention. However, insights into the response of bacterial communities to HMs in coastal sediments of India remain scarce. Here, we analyzed HMs content in three areas, along the southern coastal region of India. Based on the calculated pollution indices viz., enrichment factor (EF), contamination factor (CF), geo-accumulation index (Igeo) and sediment quality guidelines (SQGs), the studied areas were classified as uncontaminated, moderately contaminated and significantly contaminated. To explore the response of bacterial community to HMs, sediment-associated microbiota was investigated using high-throughput 16S rRNA gene amplicon sequencing. The obtained metataxonomic results revealed that bacterial diversity and community composition varied considerably in significantly contaminated area than moderately contaminated and uncontaminated areas. Proportion of bacterial classes was higher for Gammaproteobacteria, Betaproteobacteria and Actinobacteria, but lower for Alphaproteobacteria and Flavobacteriia in significantly contaminated area. Also, samples of significantly contaminated area were dominated by well-documented metal-resistant bacterial genera such as Ralstonia and Arthrobacter. Canonical correspondence analysis (CCA) showed that spatial variability of bacterial community composition was strongly correlated with HMs content such as Chromium, Cadmium and Nickel. Further analysis using PICRUSt programme indicated that the predictive functional profile also varied considerably in significantly contaminated area. By linking HMs with bacterial compositional variations, the present study highlights the likely influence of HMs in shaping sedimentary microbiota of coastal regions.

Sediment-associated bacterial community and predictive functionalities are influenced by choice of 16S ribosomal RNA hypervariable region(s): An amplicon-based diversity study.

Meta-omics approaches such as high-throughput sequencing of 16S hypervariable region(s) [HVR(s)] is extensively applied for profiling microbial community. Several studies have deciphered the influence of HVR(s) on bacterial diversity; most of these were devoted to human body habitats. Extent to which targeted HVR(s) influences the diversity estimates of environmental samples is rather unclear. Here, we evaluated the performance of five widely used universal primer pairs spanning V1-V3, V3-V4, V4, V5-V6 and V7-V9 HVRs to characterize bacterial diversity and predictive functionality of complex marine sediments. Obtained results revealed that the HVR(s) V4 and V5-V6 represented the higher species richness than others while, V1-V3 and V7-V9 were unsuccessful to detect Bacteroidetes and Planctomycetes. Further, PICRUSt analysis showed that the selected HVR(s) also had significant impact on the predictive functional profile. Conclusively, this study proved that HVR selection has a profound effect on overall results and thus should be selected with utmost caution.

3-Hydroxy coumarin demonstrates anti-biofilm and anti-hyphal efficacy against Candida albicans via inhibition of cell-adhesion, morphogenesis, and virulent genes regulation.

Candida albicans, a common fungus of human flora, can become an opportunistic pathogen and causes invasive candidiasis in immunocompromised individuals. Biofilm formation is the prime cause of antibiotic resistance during C. albicans infections and treating biofilm-forming cells is challenging due to their intractable and persistent nature. The study intends to explore the therapeutic potential of naturally produced compounds by competitive marine bacteria residing in marine biofilms against C. albicans biofilm. To this end, 3-hydroxy coumarin (3HC), a compound identified from the cell-free culture supernatant of the marine bacterium Brevundimonas abyssalis, was found to exhibit anti-biofilm and anti-hyphal activity against both reference and clinical isolates of C. albicans. The compound demonstrated significant inhibitory effects on biofilms and impaired the yeast-to-hyphal transition, wrinkle, and filament morphology at the minimal biofilm inhibitory concentration (MBIC) of 250 µg mL-1. Intriguingly, quantitative PCR analysis of 3HC-treated C. albicans biofilm revealed significant downregulation of virulence genes (hst7, ume6, efg1, cph1, ras1, als1) associated with adhesion and morphogenesis. Moreover, 3HC displayed non-fungicidal and non-toxic characteristics against human erythrocytes and buccal cells. In conclusion, this study showed that marine biofilms are a hidden source of diverse therapeutic drugs, and 3HC could be a potent drug to treat C. albicans infections.

Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system.

Biofloc technology is increasingly recognised as a sustainable aquaculture method. In this technique, bioflocs are generated as microbial aggregates that play pivotal roles in assimilating toxic nitrogenous substances, thereby ensuring high water quality. Despite the crucial roles of the floc-associated bacterial (FAB) community in pathogen control and animal health, earlier microbiota studies have primarily relied on the metataxonomic approaches. Here, we employed shotgun sequencing on eight biofloc metagenomes from a commercial aquaculture system. This resulted in the generation of 106.6 Gbp, and the reconstruction of 444 metagenome-assembled genomes (MAGs). Among the recovered MAGs, 230 were high-quality (≥90% completeness, ≤5% contamination), and 214 were medium-quality (≥50% completeness, ≤10% contamination). Phylogenetic analysis unveiled Rhodobacteraceae as dominant members of the FAB community. The reported metagenomes and MAGs are crucial for elucidating the roles of diverse microorganisms and their functional genes in key processes such as nitrification, denitrification, and remineralization. This study will contribute to scientific understanding of phylogenetic diversity and metabolic capabilities of microbial taxa in aquaculture environments.

Complete genome sequence of Halomonas boliviensis strain kknpp38, a chlorine-resistant bacterium isolated from the early-stage marine biofilm.

H. boliviensis strain kknpp38 is a dense exopolysaccharide (EPS) producing bacterium, isolated from the early-stage (72-h-old) of marine biofilm. Laboratory experiments demonstrated that this isolate forms a potent biofilm on various artificial substrata viz. polystyrene, stainless steel as well as titanium and possesses high tolerance to chlorine disinfection. To determine the genes and biosynthetic pathways involved in the EPS production, whole-genome sequencing was performed using high-throughput Illumina tag sequencing. The high-quality reads were first de novo assembled using Unicycler genome assembler (version 0.4.9b) and then annotated using Prokka (version 1.13). The complete genome comes from one circular chromosome containing 4.96 Mbp DNA with G + C content of 55%, and encompasses genes encoding 4476 proteins, 2 rRNAs, and 57 tRNAs. Intriguingly, genomic analysis revealed the existence of genes involved in ATP-binding cassette (ABC) transporter-dependent EPS biosynthesis pathways (ugd, ugd2, galU). In addition, we identified genes involved in ectoine (ectA, ectB, ectC, ectD) and polyhydroxyalkanoates (PHAs; fabA, fabB, fabD, fabF, fabH, fabV, fabZ, phaC, phaD, phaG, phaR, phaZ1) production, which are known to involve in bacterial adaptation in saline environment. The outcomes of this study expand scientific understanding on the genes and pathways involved in EPS biosynthesis by marine bacteria.

Exploring bacterioplankton communities and their temporal dynamics in the rearing water of a biofloc-based shrimp (Litopenaeus vannamei) aquaculture system.

Biofloc technology (BFT) has recently gained considerable attention as a sustainable method in shrimp aquaculture. In a successful BFT system, microbial communities are considered a crucial component in their ability to both improve water quality and control microbial pathogens. Yet, bacterioplankton diversity in rearing water and how bacterioplankton community composition changes with shrimp growth are rarely documented. In this study, the Pacific white shrimp, Litopenaeus vannamei was cultivated in a greenhouse-enclosed BFT system. Rearing water samples were collected on a weekly basis for 5 months (152 days) and water quality variables such as physicochemical parameters and inorganic nutrients were monitored. In parallel, 16S rRNA gene pyrosequencing was employed to investigate the temporal patterns of rearing-water microbiota. The productivity, survival rate, and feed conversion ratio were 3.2-4.4 kg/m3, 74%-89%, and 1.2-1.3, respectively, representing successful super-intensive cultures. The metataxonomic results indicated a highly dynamic bacterioplankton community, with two major shifts over the culture. Members of the phylum Planctomycetes dominated in rearing water during the early stages, while Actinobacteria dominated during the middle stages, and Chloroflexi and TM7 dominated during the late stages of culture. The bacterioplankton community fluctuated more in the beginning but stabilized as the culture progressed. Intriguingly, we observed that certain bacterioplankton groups dominated in a culture-stage-specific manner; these groups include Rhodobacteraceae, Flavobacteriaceae, Actinobacteria, and Chloroflexi, which either contribute to water quality regulation or possess probiotic potential. Altogether, our results indicate that an operationally successful BFT-based aquaculture system favors the growth and dynamics of specific microbial communities in rearing water. Our study expands the scientific understanding of the practical utilization of microbes in sustainable aquaculture. A thorough understanding of rearing-water microbiota and factors influencing their dynamics will help to establish effective management strategies.

Draft Genome Sequencing of Pseudoalteromonas tetraodonis Strain kknpp56, a Potent Biofilm-Forming Bacterium Isolated from Early-Stage Marine Biofilm.

Pseudoalteromonas tetraodonis strain kknpp56 is an exopolysaccharide (EPS)-producing marine bacterium that forms potent biofilm. To determine the biosynthesis pathways involved in the EPS production of this bacterium, whole-genome sequencing was performed. The complete genome comes from one chromosome containing 3.72 Mbp of DNA with a G+C content of 41%.

Thermal discharge-induced seawater warming alters richness, community composition and interactions of bacterioplankton assemblages in a coastal ecosystem.

Despite accumulating evidence on the impact of global climate warming on marine microbes, how increasing seawater temperature influences the marine bacterioplankton communities is elusive. As temperature gradient created by thermal discharges provides a suitable in situ model to study the influence of warming on marine microorganisms, surface seawater were sampled consecutively for one year (September-2016 to August-2017) from the control (unimpacted) and thermal discharge-impacted areas of a coastal power plant, located in India. The bacterioplankton community differences between control (n = 16) and thermal discharge-impacted (n = 26) areas, as investigated using 16S rRNA gene tag sequencing revealed reduced richness and varied community composition at thermal discharge-impacted areas. The relative proportion of Proteobacteria was found to be higher (average ~ 15%) while, Bacteroidetes was lower (average ~ 10%) at thermal discharge-impacted areas. Intriguingly, thermal discharge-impacted areas were overrepresented by several potential pathogenic bacterial genera (e.g. Pseudomonas, Acinetobacter, Sulfitobacter, Vibrio) and other native marine genera (e.g. Marinobacter, Pseudoalteromonas, Alteromonas, Pseudidiomarina, Halomonas). Further, co-occurrence networks demonstrated that complexity and connectivity of networks were altered in warming condition. Altogether, results indicated that increasing temperature has a profound impact on marine bacterioplankton richness, community composition, and inter-species interactions. Our findings are immensely important in forecasting the consequences of future climate changes especially, ocean warming on marine microbiota.

Bacterial community structure of early-stage biofilms is dictated by temporal succession rather than substrate types in the southern coastal seawater of India.

Bacterial communities colonized on submerged substrata are recognized as a key factor in the formation of complex biofouling phenomenon in the marine environment. Despite massive maritime activities and a large industrial sector in the nearshore of the Laccadive Sea, studies describing pioneer bacterial colonizers and community succession during the early-stage biofilm are scarce. We investigated the biofilm-forming bacterial community succession on three substrata viz. stainless steel, high-density polyethylene, and titanium over 15 days of immersion in the seawater intake area of a power plant, located in the southern coastal region of India. The bacterial community composition of biofilms and peripheral seawater were analyzed by Illumina MiSeq sequenced 16S rRNA gene amplicons. The obtained metataxonomic results indicated a profound influence of temporal succession over substrate type on the early-stage biofilm-forming microbiota. Bacterial communities showed vivid temporal dynamics that involved variations in abundant bacterial groups. The proportion of dominant phyla viz. Proteobacteria decreased over biofilm succession days, while Bacteroidetes increased, suggesting their role as initial and late colonizers, respectively. A rapid fluctuation in the proportion of two bacterial orders viz. Alteromonadales and Vibrionales were observed throughout the successional stages. LEfSe analysis identified specific bacterial groups at all stages of biofilm development, whereas no substrata type-specific groups were observed. Furthermore, the results of PCoA and UPGMA hierarchical clustering demonstrated that the biofilm-forming community varied considerably from the planktonic community. Phylum Proteobacteria preponderated the biofilm-forming community, while the Bacteroidetes, Cyanobacteria, and Actinobacteria dominated the planktonic community. Overall, our results refute the common assumption that substrate material has a decisive impact on biofilm formation; rather, it portrayed that the temporal succession overshadowed the influence of the substrate material. Our findings provide a scientific understanding of the factors shaping initial biofilm development in the marine environment and will help in designing efficient site-specific anti-biofouling strategies.

Culture dependent and independent analysis and appraisal of early stage biofilm-forming bacterial community composition in the Southern coastal seawater of India.

Microbial aggregation on artificial surfaces is a fundamental phenomenon in aquatic systems that lead to biofouling, corrosion and influence the buoyancy of plastic materials. Despite the maritime activities and with nearshore large industrial sector, Laccadive Sea in the Indian Ocean has rarely been investigated for characterizing early biofilm-forming bacterial community. The present investigation was aimed to catalogue the primary colonizers on artificial surfaces and their comparison with planktonic community in southern coastal seawater of India. Surface seawater samples and biofilm assembled on three artificial surfaces over a period of 72 h of immersion in the intake area of a nuclear power plant at Kudankulam, India were collected. The structure of surface assemblages and plankton were unveiled by employing culture dependent, DGGE and NGS methods. In static condition, a collection of aerobic heterotrophic bacteria was screened in vitro for their ability to form potent biofilm. Proteobacteria preponderated the communities both in seawater and natural biofilm and Gammaproteobacteria accounted for >85% in the latter. Vibrionaceae, Alteromonadaceae and Pseudoalteromonadaceae dominated the biofilm community and constituted for 41, 25 and 8%, respectively. In contrast to other studies that showed Rhodobacteraceae family of Alphaproteobacteria as predominant component, we found Vibrionaceae of Gammaproteobacteria as dominant group in early stage of biofilm formation. Both DGGE and NGS data indicated that the attached community is noticeably distinct from those suspended in water column and form the basis for the proposed hypothesis of species sorting theory, that is, the local environmental conditions influence bacterial community assembly. Collectively, the data are testament for species sorting process that occur during initial assembly of bacterial community in marine environment and shed light on the structure of marine bacterial biofilm development. The outcome of the present study is of immense importance for designing long-term, efficient and appropriate strategies to control the biofouling phenomenon.