Free-living and aggregate-associated Planctomycetes in the Black Sea

Abstract

We examined the distribution of uncultured Planctomycetes phylotypes along depth profiles spanning the redox gradient of the Black Sea suboxic zone to gain insight into their respective ecological niches. Planctomycetes phylogeny correlated with depth and chemical profiles, implying similar metabolisms within phylogenetic groups. A suboxic zone sample was split into > 30 and < 30 μm fractions to examine putative aggregate-attached and free-living Planctomycetes. All identified Planctomycetes were present in the > 30 μm fraction except for members of the Scalindua genus, which were apparently free-living. Sequences from Candidatus Scalindua, known to carry out the anammox process, formed two distinct clusters with nonoverlapping depth ranges. One cluster, only 97.1% similar to the named species, was present at high nitrite/nitrate and low ammonium concentrations in the upper suboxic zone. We propose this sequence type be named 'Candidatus Scalindua richardsii'. A second cluster, containing sequences more similar to 'Candidatus Scalindua sorokinii', was present at high ammonium and low nitrite conditions in the lower suboxic zone. Sequences obtained from the sulfidic zone (1000 m depth) yielded Planctomycetes from two uncharacterized Planctomycetacia clusters and three potentially new genera as well as sequences from the uncultured OP3 phylum.

Metagenomic analysis of size-fractionated picoplankton in a marine oxygen minimum zone

“…Consistent with several prior studies of particleassociated bacteria (DeLong et al, 1993;Fuchsman et al, 2012), Deltaproteobacteria were significantly enriched on prefilters. Although this group was a negligible component of both size fractions at the surface (o0.1% of total sequences at 5 m), deltaproteobacterial sequences increased in relative abundance in both fractions by 70 m, and were 8-to 28-fold more abundant in prefilters from 70 m down to 1000 m, representing up to 3% of total sequences in the larger size fraction (Supplementary Figure S8).…”

“…Of the sequences assignable to a Genus, 54% matched the Genus Planctomyces, with the vast majority of these being detected only in the prefilters where Planctomyces were enriched on average 75-fold compared with the Sterivex fraction. This pattern agrees with genetic and isolation-based studies identifying surface attachment as a key life history state for diverse Planctomycete genera, including Planctomyces (Bauld and Staley, 1976;Morris et al, 2006;Bengtsson and Øvreås, 2010) and with a general Planctomycetes enrichment in particle-associated microbial cell fractions (DeLong et al, 1993;Fuchsman et al, 2011Fuchsman et al, , 2012. Although the 16S amplicon pool provided limited phylogenetic resolution for some taxonomic groups discussed here, additional insight into the composition of key OMZ clades can be provided by analyzing the taxonomic identification of protein-coding genes (see Metagenome data below).…”

“…Analyses with genus-specific FISH probes previously showed that a minor fraction of total Candidatus Scalindua cells in the Namibian and ETSP OMZs associates directly with particles (Woebken et al, 2007), consistent with our data. In contrast, marker gene surveys from the suboxic Black Sea detected this genus in the 0.2-30 mm fraction but not in the larger particle-associated fraction above 30 mm (Fuchsman et al, 2012). As Candidatus Scalindua is presumed to be the primary lineage responsible for anammox in OMZs (Woebken et al, 2008;Galan et al, 2012), these patterns suggest that the bulk of anammox-capable cells in OMZs may be spatially separated at the microscale from potentially linked metabolic transformations on particles, for example, nitrite production and ammonia remineralization by heterotrophic denitrifiers.…”

“…However, certain taxonomic groups with important functional roles in OMZ elemental cycling may differ in abundance and activity between freeliving versus particle-associated communities. Recent diversity surveys based on 16S rRNA gene sequences confirm distinct taxon compositions among size-fractionated samples (30 mm cutoff) from the suboxic water column of the Black Sea (Fuchsman et al, 2011(Fuchsman et al, , 2012. Notably, members of the Alphaproteobacteria (for example, SAR11-like sequences) and the marine anammox planctomycete Candidatus Scalindua were significantly enriched in the smaller size fraction, while key anaerobic lineages, including members of the sulfate-reducing Deltaproteobacteria were more abundant in the larger, particle-associated fraction (430 mm).…”

Size-fraction partitioning of community gene transcription and nitrogen metabolism in a marine oxygen minimum zone

“…Sequences matching the anammox Planctomycete Candidatus Scalindua (Order Brocadiales) were also confined primarily to the FL fraction, peaking at 14.1% of total FL amplicons at 300 m, compared with 0.3-1.5% in PA fractions. Anammox bacteria were previously shown to be enriched in the smallest size fractions in studies of the Chilean OMZ (Ganesh et al, 2014), the Black Sea (Fuchsman et al, 2012), and an OMZ off Costa Rica (Kong et al, 2013), but have also been Size-fractionated gene transcription and N cycling S Ganesh et al detected in direct contact with particles in oxygendepleted waters over the Namibian shelf (Woebken et al, 2007). The composition of the ETNP bacterial community with potential roles in coupled N and sulfur cycles differed from that of other OMZs and varied among size fractions.…”