High overall diversity and dominance of microdiverse relationships in salt marsh sulphate‐reducing bacteria

Abstract

The biogeochemistry of North Atlantic salt marshes is characterized by the interplay between the marsh grass Spartina and sulphate-reducing bacteria (SRB), which mineralize the diverse carbon substrates provided by the plants. It was hypothesized that SRB populations display high diversity within the sediment as a result of the rich spatial and chemical structuring provided by Spartina roots. A 2000-member 16S rRNA gene library, prepared with delta-proteobacterial SRB-selective primers, was analysed for diversity patterns and phylogenetic relationships. Sequence clustering detected 348 16S rRNA sequence types (ribotypes) related to delta-proteobacterial SRB, and it was estimated that a total of 623 ribotypes were present in the library. Similarity clustering showed that approximately 46% of these sequences fell into groups with < 1% divergence; thus, microheterogeneity accounts for a large portion of the observable genetic diversity. Phylogenetic comparison revealed that sequences most frequently recovered were associated with the Desulfobacteriaceae and Desulfobulbaceae families. Sequences from the Desulfovibrionaceae family were also observed, but were infrequent. Over 80% of the delta-proteobacterial ribotypes clustered with cultured representatives of Desulfosarcina, Desulfococcus and Desulfobacterium genera, suggesting that complete oxidizers with high substrate versatility dominate. The large-scale approach demonstrates the co-existence of numerous SRB-like sequences and reveals an unexpected amount of microdiversity.

Effects of ciprofloxacin on salt marsh sediment microbial communities

“…The dominating presence of Desulfobacter biomarkers in all controls, with a low abundance of Desulfobulbus and no evidence of Desulfovibrio is consistent with SRB distribution reported previously in salt marshes. Desulfobacteriaceae associated sequences accounted for over 80% of the recovered sequences, while less than 1% out of 1650 sequences were assigned to Desulfovibrio in a salt marsh study (Klepac-Ceraj et al, 2004). The dominance of Desulfobacteriaceae in salt marsh communities has also been confirmed by other groups (Devereux et al, 1996;Rooney-Varga et al, 1998).…”

Low Intraspecific Diversity in a Polynucleobacter Subcluster Population Numerically Dominating Bacterioplankton of a Freshwater Pond

“…Only a few studies have revealed the microdiversity of free-living bacterial populations (1,29,42,45). The investigated PnecC population differed from these populations in a low microdiversity and a strongly uneven population structure.…”

“…Recently, Acinas et al (1) demonstrated by the construction and analysis of 16S rRNA clone libraries that a coastal bacterioplankton community contained a very high diversity of ribotypes, the vast majority of which fell into phylogenetically microdiverse sequence clusters (Ͻ1% divergent 16S rRNA sequences). Similarly, extensive microdiversities were also observed in populations of sulfate-reducing bacteria inhabiting a salt marsh (29) and in a Vibrio splendidus population from coastal bacterioplankton (42). The V. splendidus population consisted of at least a thousand distinct genotypes, which demonstrated a high variability in genome size and allelic composition (42).…”

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

“…This has only recently become possible but has already revealed fine-scale patterns of differentiation within ribotype sequences, which suggest prevalence of natural clusters with 1% internal sequence divergence. In both coastal bacterioplankton and marsh sediment sulphate-reducing bacteria samples, most sequences fell into such microdiverse sequence clusters indicating predominance of closely related taxa (Acinas et al 2004;Klepac-Ceraj et al 2004). Indeed, it has been proposed that sequence clusters may represent natural units of differentiation equivalent to populations or species (Cohan 2002).…”