Insensitivity of Diverse and Temporally Variable Particle-Associated Microbial Communities to Bulk Seawater Environmental Parameters

Abstract

There is a growing recognition of the roles of marine microenvironments as reservoirs of biodiversity and as sites of enhanced biological activity and in facilitating biological interactions. Here, we examine the bacterial community inhabiting free-living and particle-associated seawater microenvironments at the Pivers Island Coastal Observatory (PICO). 16S rRNA gene libraries from monthly samples (July 2013 to August 2014) were used to identify microbes in seawater in four size fractions: >63 m (zooplankton and large particles), 63 to 5 m (particles), 5 to 1 m (small particles/dividing cells), and <1 m (free-living prokaryotes). Analyses of microbial community composition highlight the importance of the microhabitat (e.g., particle-associated versus free-living lifestyle) as communities cluster by size fraction, and the microhabitat explains more of the community variability than measured environmental parameters, including pH, particle concentration, projected daily insolation, nutrients, and temperature. While temperature is statistically associated with community changes in the <1-m and 5-to 1-m fractions, none of the measured bulk seawater environmental variables are statistically significant in the larger-particle-associated fractions. These results, combined with high particle-associated community variability, especially in the largest size fraction (i.e., >63 m), suggest that particle composition, including eukaryotes and their associated microbiomes, may be an important factor in selecting for specific particle-associated bacteria. IMPORTANCEBy comparing levels of particle-associated and free-living bacterial diversity at a coastal location over the course of 14 months, we show that bacteria associated with particles are generally more diverse and appear to be less responsive to commonly measured environmental variables than free-living bacteria. These diverse and highly variable particle-associated communities are likely driven by differences in particle substrates both within the water column at a single time point and due to seasonal changes over the course of the year.

Microbial communities across nearshore to offshore coastal transects are primarily shaped by distance and temperature

“…Although GJAM clusters are generally distributed across the phylogenetic tree, a majority (18/20) of Bacteriodetes are assigned to nearshore clusters (e.g. Clusters 1, 4 and 7), which is consistent with their predicted role in degrading complex organic matter and associations with algae and other particles (Fernández-Gomez et al, 2013;Yung et al, 2016) as well as observations in the Columbia River Estuary system (Fortunato et al, 2013). Although we focus on the influence of distance along the transect, some GJAM clusters revealed temperature-only associations; for example, three of the four OTUs in SAR406 were positively associated with temperature (Cluster 8; Supporting Information Fig.…”

“…Genomic DNA was subsequently cleaned using the Zymo OneStep PCR inhibitor removal kit and DNA was quantified using a Nanodrop ND-100. 16S rRNA genes from each sample were sequenced, using a dual-index sequencing approach as described previously (Kozich et al, 2013;Yung et al, 2016). PCR reactions contained 10 ng of template DNA, 1.25 U Econo Taq (Lucigen) and a final concentration of 1× Taq buffer, 200 μM dNTPs, 2 mM MgCl 2 and 0.5 μM of each primer.…”

Annual community patterns are driven by seasonal switching between closely related marine bacteria

“…Microbial communities were characterized using a dual index amplicon library approach targeting the 16S rRNA gene V3-V4 region (Kozich et al, 2013;Yung et al, 2016). PCR reactions contained 20 ng of template gDNA and 0.4 U of Q5 DNA polymerase (NEB, Ipswich, MA, USA) as well as a final concentration of 200 μM dNTPs, 2 mM MgCl 2 and 0.5 μM of each primer.…”

Characterization of particle-associated and free-living bacterial and archaeal communities along the water columns of the South China Sea

“…In particularly, some broad key functional gene categories involved in DOM utilization (Poretsky et al, 2010;Rinta-Kanto et al, 2012) and specific functional gene groups linked to successive decomposition of phytoplankton blooms (Teeling et al, 2012) are significantly different, indicating the fundamental differences in survival strategies in relation to potentially available substrates. It is further revealed that PA microbes generally have larger genomes with a variety of metabolic and regulatory capabilities of utilizing compositionally varied organic matter, while the genomes of FL microbes usually are smaller with streamlined metabolic and regulatory functions that enable efficient adaption to oligotrophic conditions (Smith et al, 2013;Yawata et al, 2014;Yung et al, 2016). Phylogenetically, PA and FL lineages generally exhibit different compositions.…”

“…Actually, most members of the PA and FL clades are generalists which switch their lifestyles via attachment and detachment to particles (Crespo et al, 2013;Li et al, 2015). As revealed in many marine niches, α-Proteobacteria, γ-Proteobacteria and Bacteriodetes are the major overlapped phyla in both PA and FL microbial fractions (Yung et al, 2016).…”