Structuring of Bacterioplankton Diversity in a Large Tropical Bay

Abstract

Structuring of bacterioplanktonic populations and factors that determine the structuring of specific niche partitions have been demonstrated only for a limited number of colder water environments. In order to better understand the physical chemical and biological parameters that may influence bacterioplankton diversity and abundance, we examined their productivity, abundance and diversity in the second largest Brazilian tropical bay (Guanabara Bay, GB), as well as seawater physical chemical and biological parameters of GB. The inner bay location with higher nutrient input favored higher microbial (including vibrio) growth. Metagenomic analysis revealed a predominance of Gammaproteobacteria in this location, while GB locations with lower nutrient concentration favored Alphaproteobacteria and Flavobacteria. According to the subsystems (SEED) functional analysis, GB has a distinctive metabolic signature, comprising a higher number of sequences in the metabolism of phosphorus and aromatic compounds and a lower number of sequences in the photosynthesis subsystem. The apparent phosphorus limitation appears to influence the GB metagenomic signature of the three locations. Phosphorus is also one of the main factors determining changes in the abundance of planktonic vibrios, suggesting that nutrient limitation can be observed at community (metagenomic) and population levels (total prokaryote and vibrio counts).

Occurrence, seasonality and infectivity of Vibrio strains in natural populations of mussels Mytilus galloprovincialis

“…As expected, the composition of the Vibrio communities in Alcabre and the Sor River differed. Our results agree with the established hypothesis that Vibrio population diversity is complex and is controlled by fluctuations in physiochemical parameters and by the abundance and composition of Vibrio reservoirs (Maugeri et al 2004, Thomp son et al 2004, Turner et al 2009, Gregoracci et al 2012. Other Vibrio species associated with bivalve cultures, including V. anguillarum, V. tapetis, V. diabolicus, V. fortis, V. noatunensis and V. sina loensis (Castro et al 2002, Beaz-Hidalgo et al 2010, have been detected in natural mussel populations.…”

Metagenomic analysis reveals microbial diversity and function in the rhizosphere soil of a constructed wetland

“…For function annotation, we focused on the metabolism of xenobotic compounds, N and heavy metals (iron and manganese). For xenobotic compounds and N, SEED subsystems and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation in MG-RAST with parameters [21] (minimum alignment length, 15 amino acids and E-value cutoffs, 1e-5) were used to identify sequences to different functional groups (SEED) or metabolic pathways (KEGG). Metabolic genes present in water and soil were identified and the abundances of those gene sequences were calculated.…”

Using high-throughput sequencing to assess the impacts of treated and untreated wastewater discharge on prokaryotic communities in an urban river

“…anl.gov/) for function annotation using MG-RAST pipeline (Meyer et al 2008). We used SEED subsystem and KEGG (Kyoto Encyclopedia of Genes and Genomes) annotation to assign reads to different functional groups (SEED) or metabolic pathways (KEGG) in MG-RAST with recommended parameters (Gregoracci et al 2012) (minimum alignment length, 15 amino acids; E-value cutoffs, 1e-5). Xenobiotics and nitrogen biodegradation or biotransformation genes present in five samples were identified and compared using the KEGG database.…”