16S rRNA gene amplicon-based metagenomic analysis of bacterial communities in the rhizospheres of selected mangrove species from Mida Creek and Gazi Bay, Kenya

Abstract

Prokaryotic communities play key roles in biogeochemical transformation and cycling of nutrients in the productive mangrove ecosystem. In this study, the vertical distribution of rhizosphere bacteria was evaluated by profiling the bacterial diversity and community structure in the rhizospheres of four mangrove species (Sonneratia alba, Rhizophora mucronata, Ceriops tagal and Avicennia marina) from Mida Creek and Gazi Bay, Kenya, using DNA-metabarcoding. Alpha diversity was not significantly different between sites, but, significantly higher in the rhizospheres of S. alba and R. mucronata in Gazi Bay than in Mida Creek. Chemical parameters of the mangrove sediments significantly correlated inversely with alpha diversity metrics. The bacterial community structure was significantly differentiated by geographical location, mangrove species and sampling depth, however, differences in mangrove species and sediment chemical parameters explained more the variation in bacterial community structure. Proteobacteria (mainly Deltaproteobacteria and Gammaproteobacteria) was the dominant phylum while the families Desulfobacteraceae, Pirellulaceae and Syntrophobacteraceae were dominant in both study sites and across all mangrove species. Constrained redundancy analysis indicated that calcium, potassium, magnesium, electrical conductivity, pH, nitrogen, sodium, carbon and salinity contributed significantly to the species–environment relationship. Predicted functional profiling using PICRUSt2 revealed that pathways for sulfur and carbon metabolism were significantly enriched in Gazi Bay than Mida Creek. Overall, the results indicate that bacterial community composition and their potential function are influenced by mangrove species and a fluctuating influx of nutrients in the mangrove ecosystems of Gazi Bay and Mida Creek.

Structural and Predicted Functional Diversities of Bacterial Microbiome in Response to Sewage Sludge Amendment in Coastal Mudflat Soil

“…These results were in agreement with findings of Xie et al [ 3 ], who suggested that organic amendments with abundant nutrients not only directly affect soil carbon and nitrogen cycling processes, but also had an enormous impact on microbial species and activities, which in turn affected the C- and N-relevant transformations. For instance, significantly positive relationships among nutrients and pronounced core families of Hyphomicrobiaceae , Cytophagaceae , Pirellulaceae , Microbacteriaceae , and Phyllobacteriaceae were observed in our study ( Figure 3 A and Figure 5 ), suggesting the enhanced carbon and nitrogen biogeochemical processes in soils after sewage sludge usage, as these families have been widely reported to be capable of participating in relevant functions [ 109 , 110 , 111 , 112 ]. Together, these outcomes suggested that sewage sludge significantly improved the diversity of the bacterial community and functionality mainly by ameliorating microhabitats in coastal mudflat soil, which harbored alleviated saline–alkali conditions and promoted available nutrients.…”

Halalkalibacterium roseum gen. nov., sp. nov., a new member of the family Balneolaceae isolated from soil

“…demonstrated that the surrounding soils of corroded pipelines without petroleum contamination contained significantly more abundant Balneolaceae members ( Balneola and KSA1) [17]. The 16S rRNA gene amplicon-based metagenomic analysis revealed that Balneolaceae and some other bacterial groups were enriched differentially in the rhizosphere of Avicennia marina [18]. In this study, we report a novel moderately halophilic bacterium affiliated with Balneolaceae and establish its taxonomic position by using polyphasic approaches.…”

Analysis and Interpretation of metagenomics data: an approach

“…Bacterial wilt disease in Cucurbita maxima in China caused by Ralstonia solanacearum was identified using 16S rRNA gene sequencing of the isolates collected from the plants infected by wilt disease [ 33 ]. A recent study with 16S rRNA gene amplicon metagenomic analysis resulted in the identification of a rhizospheric microbial community of plants like Eichhornia crassipes [ 34 ] and mangrove species ( Sonneratia alba, Rhizophora mucronata, Ceriops tagal , and Avicennia marina ) [ 35 ].…”