Indigenous bacterial community of heavy metal tolerance in the rhizosphere soils of Mimosa pudica naturally growing on an ex-tin mining area

Aims@#The purpose of this research was to explore the composition and genomic functions of bacterial community inhabiting the rhizosphere of Mimosa pudica, which were naturally growing on tailing and non-tailing soils of an ex-tin mining area.@*Methodology and results@#DNA were extracted from rhizosphere soils and PCR targeting the hypervariable region V3-V4 was carried out by Illumina 16S metagenomic library. Libraries were sequenced using Illumina MiSeq. The Operational Taxonomic Units (OTUs) were assigned to 23 bacterial phyla, 72 classes, 165 orders, 248 families and 357 genera. The most represented and dominant phylum was Proteobacteria, with an average abundance value of 41.2%. The most represented genera included Paraburkholderia, Bradyrhizobium, Bacillus, Candidatus, Acidothermus, Acidibacter and Nitrospira. Non-tailing soils had more number and richness of species while the tailings had more diversity of species. The metagenomes accommodate suspected genes for heavy metal tolerance of microbes (As, Cr, Co, Zn, Ni, Cu, Cd, Fe and Hg) and microbial plant-growth-promoting traits for hyperaccumulator plants (synthesis of indole acetic acid (IAA), siderophore and 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase; solubilization of phosphate and potassium and nitrogen fixation). @*Conclusion, significance and impact of study@#Bacteria and predicted genes discovered could be part of major factors influencing growth of M. pudica in heavy metal-contaminated soils. The study provides the first report and a basis into the bacterial community associated with M. pudica in ex-tin mining soils from the studied geographical location. The findings also provide fundamental knowledge on phytoremediation potential of heavy metal contaminated soils involving indigenous beneficial microbial populations.

Bacterial diversity on wild shrimp post larvae in a mangrove biodiversity hotspot

Aims@#This study aims to assess the impact of anthropogenic activities on shrimp microbiome in a biodiverse mangrove forest ecosystem, along the Merbok River, Kedah, Malaysia.@*Methodology and results@#To assess the impacts, a microbiome study of wild post larvae shrimps along the river was conducted as a health indicator of the shrimp hosts which in turn would reflect the river conditions. A 16S rRNA gene amplicon sequencing of the wild post larvae shrimp microbiomes sampled across areas of varying human activities was conducted. Samples were obtained from four sites ranging from upstream river habitat to downstream brackish water towards the marine coast. Individuals detected from the sequence were then counted and their relative abundance of bacterial diversity were compared. All abundances are up to 100% and the diversity indices were calculated using proportions of each species. The Operational Taxonomy Unit (OTUs) were obtained by using USEARCH and UPARSE software. Twenty-eight bacterium phyla were detected, dominated by phyla Proteobacteria, Actinobacteria, Firmicutes and Bacteroidetes at each site. Eighteen families were dominant at each site with Streptomycetaceae being the major abundant. At the genus level, the most abundant genera were Streptomyces sp., Mesorhizobium sp., Rhizobium sp., Bacillus sp. and Pseudomonas sp.@*Conclusion, significance and impact of study@#In general, the diversity of opportunistic and coliform bacteria was low. Thus, despite being exposed to various levels of human activities, the Merbok River and its mangrove surroundings still serve as a good spawning and nursery sites of shrimps and presumably other inhabitants.

The potential use of prodigiosin as a shrimp feed additive and its dynamic influence on the shrimp gut microbial community – an in vitro gut model

Aims@#A simple in vitro model system was applied in this study assessing the dynamics of the microbial community associated with the shrimp gut system to understand the changes that influence dietary variables. @*Methodology and results@#The diversity and abundance of microbiome were monitored within two different treatment slurries inoculated with shrimp faecal samples as to mimic the effect of diet manipulation, and 16S rRNA gene of MiSeq Illumina-based sequencing was applied. The different diets tested were a commercial standard diet and a prodigiosin added diet. There was very clear separation between the commercial standard diet and prodigiosin added diet as revealed by the total viable counts (TVC) and sequencing data. It suggested that the microbial community of the shrimp gut system exhibited a dynamic response with the treatments and allochthonous bacterial present. The prodigiosin added diet was clearly separated from the commercial standard diet serving as a potential shrimp feed additive. The sequencing data analysis showed that members of the genera Vibrio, Shigella and Photobacterium became predominant on the commercial standard diet treatment. The prodigiosin-added diet treatments indicated an abundance of members of the genera Micrococcus, Arthrobacter, and Shigella. @*Conclusion, significance and impact of study@#In vitro model system-based testing of diets could be a useful method to determine the potential effect of diet manipulation on shrimp gut system microbiome members.