Development of microbial enrichments for simultaneous removal of sulfur and nitrogenous metabolites in saline water aquaculture.

AIM: The aim of the study was to develop microbial enrichments from the nitrifying microbial consortia and the environment for simultaneous removal of ammonia, nitrate, and sulfide in aquaculture systems at varied salinities. METHODS AND RESULTS: Sulfur and nitrogen metabolites are the major factors affecting the farmed aquatic animal species and deteriorate the receiving environments causing ecological damage. The present study reports the development of microbial enrichments from the nitrifying microbial consortia and the environment. The enrichments used thiosulfate or thiocyanate as an energy source and simultaneously removed sulfur, ammonia, and nitrite in spiked medium (125 mg/l ammonia; 145 mg/l nitrite). Further, the microbes in the enrichments could grow up to 30 g/l salinity. Metagenomic studies revealed limited microbial diversity suggesting the enrichment of highly specialized taxa, and co-occurrence network analysis showed the formation of three micro-niches with multiple interactions at different taxonomic levels. CONCLUSIONS: The ability of the enrichments to grow in both organic and inorganic medium and simultaneous removal of sulfide, ammonia, and nitrite under varied salinities suggests their potential application in sulfur, nitrogen, and organic matter-rich aquaculture pond environments and other industrial effluents.

Diverse key nitrogen cycling genes nifH, nirS and nosZ associated with Pichavaram mangrove rhizospheres as revealed by culture-dependent and culture-independent analyses.

Mangroves are highly productive unique ecosystems harboring diverse unexplored microbial communities that play crucial roles in nutrient cycling as well as in maintaining ecosystem services. The mangrove-associated microbial communities transform the dead vegetation into nutrient sources of nitrogen, phosphorus, potash, etc. To understand the genetic and functional diversity of the bacterial communities involved in nitrogen cycling of this ecosystem, this study explored the diversity and distribution of both the nitrogen fixers and denitrifiers associated with the rhizospheres of Avicennia marina, Rhizophora mucronata, Suaeda maritima, and Salicornia brachiata of the Pichavaram mangroves. A combination of both culturable and unculturable (PCR-DGGE) approaches was adopted to explore the bacterial communities involved in nitrogen fixation by targeting the nifH genes, and the denitrifiers were explored by targeting the nirS and nosZ genes. Across the rhizospheres, Gammaproteobacteria was found to be predominant representing both nitrogen fixers and denitrifiers as revealed by culturable and unculturable analyses. Sequence analysis of soil nifH, nirS and nosZ genes clustered to unculturable, with few groups clustering with culturable groups, viz., Pseudomonas sp. and Halomonas sp. A total of 16 different culturable genera were isolated and characterized in this study. Other phyla like Firmicutes and Actinobacteria were also observed. The PCR-DGGE analysis also revealed the presence of 29 novel nifH sequences that were not reported earlier. Thus, the mangrove ecosystems serve as potential source for identifying unexplored novel microbial communities that contribute to nutrient cycling.

16 S rRNA gene diversity and gut microbial composition of the Indian white shrimp (Penaeus indicus).

The endemic Indian white shrimp (Penaeus indicus) is an economically important crustacean species, distributed in the Indo-West Pacific region. Knowledge of its gut microbial composition helps in dietary interventions to ensure improved health and production. Here we analyzed V3-V4 hypervariable regions of the 16 S rRNA gene to examine intestinal microbiota in wild and domesticated farmed P. indicus. The study revealed that Proteobacteria, Fusobacteria, Tenericutes, and Bacteroidetes, were the dominant phyla in both the groups although there were differences in relative abundance. The dominant genera in case of the wild group were Photobacterium (29.5 %) followed by Propionigenium (13.9 %), Hypnocyclicus (13.7 %) and Vibrio (11.1 %); while Vibrio (46.5 %), Catenococcus (14 %), Propionigenium (10.3 %) and Photobacterium (8.7 %) were dominant in the farmed group. The results of the study suggest the role of environment on the relative abundance of gut bacteria. This is the first report characterizing gut microbial diversity in P. indicus, which can be used to understand the role of gut microbiota in health, nutrition, reproduction, and growth.

Microbial community profiling of ammonia and nitrite oxidizing bacterial enrichments from brackishwater ecosystems for mitigating nitrogen species.

Nitrogen species such as ammonia and nitrite are considered as major stressors in modern aquaculture practices. We developed enrichments of ammonia oxidising bacteria (AOB) and nitrite oxidising bacteria (NOB) for effective mitigation of nitrogenous wastes in the shrimp culture operations. The objective of this study was to understand the microbial community composition of AOB and NOB enrichments using the V3-V4 region of the 16S rDNA gene by Illumina MiSeq sequencing. The analysis revealed 2948 and 1069 OTUs at 97% similarity index and Shannon alpha diversity index of 7.64 and 4.85 for AOB and NOB enrichments, respectively. Comparative analysis showed that a total of 887 OTUs were common among AOB and NOB enrichments. The AOB and NOB enrichment were dominated by Eubacteria at 96% and 99.7% respectively. Proteobacterial phylum constituted 31.46% (AOB) and 39.75% (NOB) and dominated by α-Proteobacteria (20%) in AOB and γ-Proteobacteria (16%) in NOB. Among the species in AOB enrichment (2,948) two sequences were assigned to ammonia oxidising bacterial group belonging to Nitrosomonas, and Nitrosococcus genera and two belonged to archaeon group comprising Nitrosopumilus and Candidatus Nitrososphaeraea genera. The NOB enrichment was predominated by Nitrospiraceae and Thermodesulfovibrionaceae. Further, the data revealed the presence of heterotrophic bacteria contributing to the process of nitrification and form microcosm with the AOB and NOB. PICRUSt analysis predicted the presence of 24 different nitrogen cycling genes involved in nitrification, denitrification, ammonia and nitrogen transporter family, nitrate reduction and ammonia assimilation. The study confirms the presence of many lesser known nitrifying bacteria along with well characterised nitrifiers.

Diversity and N-acyl-homoserine lactone production by Gammaproteobacteria associated with Avicennia marina rhizosphere of South Indian mangroves.

The diversity of N-acyl-homoserine lactone (AHL)-producing rhizosphere bacterial community associated with Avicennia marina in the mangrove ecosystems of South India was investigated. Approximately 800 rhizobacteria were isolated from A. marina, and they were screened for the production of AHL using two biosensors, Chromobacterium violaceum CV026 and Agrobacterium tumefaciens NTL4 (pZLR4). Among the total isolates screened, 7% of the rhizobacteria showed positive induction for AHL signals. The BOX-PCR profile of 56 positive isolates represented 11 distinct genotypic groups. Phylogenetic analyses of the 16S rRNA sequences of 16 representatives showed that the isolates belonged to the class Gammaproteobacteria, which represented six different genera: Pseudomonas, Aeromonas, Vibrio, Photobacterium, Serratia and Halomonas. The study also identified three AHL-producing species, namely, Photobacterium halotolerans MSSRF QS48, Vibrio xiamenensis MSSRF QS47 and Pseudomonas sp. MSSRF QS1 that had not been reported previously. AHL profiling by TLC detected short chains C4, C6 and C8-HSL, and long chains C10 and C12-HSL with both unsubstituted and substituted side chains among the 16 representative AHL positives. This is the first report concerning the diversity of AHL-producing Gammaproteobacteria from mangrove ecosystems exhibiting diverse AHL profiles.