Spatial Variations in Microbial Community Composition in Surface Seawater from the Ultra-Oligotrophic Center to Rim of the South Pacific Gyre

Abstract

Surface seawater in the South Pacific Gyre (SPG) is one of the cleanest oceanic environments on earth, and the photosynthetic primary production is extremely low. Despite the ecological significance of the largest aquatic desert on our planet, microbial community composition in the ultra-oligotrophic seawater remain largely unknown. In this study, we collected surface seawater along a southern transect of the SPG during the Integrated Ocean Drilling Program (IODP) Expedition 329. Samples from four distinct sites (Sites U1368, U1369, U1370 and U1371) were examined, representing ∼5400 kilometers of transect line from the gyre heart to the edge area. Real-time PCR analysis showed 16S rRNA gene abundance in the gyre seawater, ranging from 5.96×105 to 2.55×106 copies ml−1 for Bacteria and 1.17×103 to 1.90×104 copies ml−1 for Archaea. The results obtained by statistic analyses of 16S rRNA gene clone libraries revealed the community composition in the southern SPG area: diversity richness estimators in the gyre center (Sites U1368 & U1369) are generally lower than those at sites in the gyre edge (Sites U1370 & U1371) and their community structures are clearly distinguishable. Phylogenetic analysis showed the predominance of Proteobacteria (especially Alphaproteobacteria) and Cyanobacteria in bacterial 16S rRNA gene clone libraries, whereas phylotypes of Betaproteobacteria were only detected in the central gyre. Archaeal 16S rRNA genes in the clone libraries were predominated by the sequences of Marine Group II within the Euryarchaeota, and the Crenarchaeota sequences were rarely detected, which is consistent with the real-time PCR data (only 9.9 to 22.1 copies ml−1). We also performed cultivation of heterotrophic microbes onboard, resulting in 18.9% of phylogenetically distinct bacterial isolates at least at the species level. Our results suggest that the distribution and diversity of microbial communities in the SPG surface seawater are closely related to the ultra-oligotrophic oceanographic features in the Pacific Ocean.

Bacterial Diversity in the South Adriatic Sea during a Strong, Deep Winter Convection Year

“…During the entire year, the euphotic zone and the mixed layer were dominated by Bacteria, while Archaea were only a minor constituent, as was found elsewhere (41,42). SAR11 was the most abundant phylogenetic group and regularly accounted for more than 40% of the communities.…”

Using Total Internal Reflection Fluorescence Microscopy To Visualize Rhodopsin-Containing Cells

“…Instead, rhodopsin abundance has been calculated based on metagenomic sequence data (3,12,24,25), amplicon sequencing (15,26,27), quantitative PCR (QPCR) (27,28), or cultivation (15,(29)(30)(31). These estimates show that in some marine environments, up to 70% of the cells may host a rhodopsin (3), while up to 30% are Chl a-containing cyanobacteria (32,33) and an additional 1 to 30% contain BChl a (34). In nonmarine aquatic environments, 35 to 62% of genomes within metagenomic assemblies harbor a rhodopsin (14), while analysis of freshwater bacterioplankton metagenomic assemblies and single amplified genomes from the same locations suggested the presence of a rhodopsin in 37 to 56% and 8 to 20% of the samples, respectively (35).…”

Bacterial Biofilm Communities and Coral Larvae Settlement at Different Levels of Anthropogenic Impact in the Spermonde Archipelago, Indonesia

“…Similar most abundant taxa were also among the most abundant on the surfaces of crustose coralline algae, CCA (Sneed et al, 2015). Cyanobacteria, which were found in highest numbers at the inshore site (LL), are often an indicator for bad water quality and eutrophic conditions (Agawina et al, 2003;Paerl et al, 2011) and may inhibit coral recruitment (Charpy et al, 2012), while Alphaproteobacteria, which had the lowest abundance at the inshore site, are often associated with more oligotrophic systems (Yin et al, 2013) and were found to be dominant on CCA surfaces, where their decrease was shown to reduce coral larvae settlement (Webster et al, 2011). These findings corroborate the assumption that the environmental conditions at the inshore site, which was most affected by anthropogenic impacts from nearby Makassar, accommodate a certain BCC accustomed to these conditions.…”