Novel acsF Gene Primers Revealed a Diverse Phototrophic Bacterial Population, Including Gemmatimonadetes, in Lake Taihu (China)

Abstract

Anoxygenic phototrophs represent an environmentally important and phylogenetically diverse group of organisms. They harvest light using bacteriochlorophyll-containing reaction centers. Recently, a novel phototrophic bacterium, Gemmatimonas phototrophica, belonging to a rarely studied phylum, Gemmatimonadetes, was isolated from a freshwater lake in the Gobi Desert. To obtain more information about the environmental distribution of phototrophic Gemmatimonadetes, we collected microbial samples from the water column, upper sediment, and deeper anoxic sediment of Lake Taihu, China. MiSeq sequencing of the 16S rRNA, pufM, and bchY genes was carried out to assess the diversity of local phototrophic communities. In addition, we designed new degenerate primers of aerobic cyclase gene acsF, which serves as a convenient marker for both phototrophic Gemmatimonadetes and phototrophic Proteobacteria. Our results showed that most of the phototrophic species in Lake Taihu belong to Alpha-and Betaproteobacteria. Sequences of green sulfur and green nonsulfur bacteria (phototrophic Chlorobi and Chloroflexi, respectively) were found in the sediment. Using the newly designed primers, we identified a diverse community of phototrophic Gemmatimonadetes forming 30 operational taxonomic units. These species represented 10.5 and 17.3% of the acsF reads in the upper semiaerobic sediment and anoxic sediment, whereas their abundance in the water column was <1%. IMPORTANCEPhotosynthesis is one of the most fundamental biological processes on Earth. Recently, the presence of photosynthetic reaction centers has been reported from a rarely studied bacterial phylum, Gemmatimonadetes, but almost nothing is known about the diversity and environmental distribution of these organisms. The newly designed acsF primers were used to identify phototrophic Gemmatimonadetes from planktonic and sediment samples collected in Lake Taihu, China. The Gemmatimonadetes sequences were found mostly in the upper sediments, documenting the preference of Gemmatimonadetes for semiaerobic conditions. Our results also show that the phototrophic Gemmatimonadetes present in Lake Taihu were relatively diverse, encompassing 30 operational taxonomic units.

Diel changes and diversity of pufM expression in freshwater communities of anoxygenic phototrophic bacteria

“…In general, APB communities in both lakes were dominated by Alpha- and Betaproteobacteria (Fig. 3), which is consistent with previous reports 16,26,27,44,45 . However, these two lakes differed largely at the OTU level, with only less than 10% of the OTUs shared between them (Fig.…”

“…The first cultured Chloroflexi were thermophilic species originating from various thermal springs 7,49,50 . In recent years, several studies registered puf M sequences belonging to phototrophic Chloroflexi in various freshwater habitats 16,22,37 . Here, we provide further evidence that freshwater phototrophic Chloroflexi were not only present, but also highly active in photosynthetic gene expression.…”

“…Diversity of the puf M gene was investigated in various aquatic habitats, including open ocean 20,21 , estuaries 22 , coastal lagoons 23 , permanently frozen lakes 24 , saline lakes 25 and freshwater lakes 26,27 . Presently, next-generation sequencing technologies enabled to explore puf M diversity to an unprecedented degree 16,28,29 .…”

Active pathways of anaerobic methane oxidation across contrasting riverbeds

“…Phylogenetic analysis showed that the M. oxyfera -like sequences recovered were 90–97% identical to the 16S rRNA gene of Candidatus Methylomirabilis oxyfera [10]. These sequences were closely related (>96% identical) to the M. oxyfera -like sequences reported in enrichment cultures [52], lake sediments [23, 58, 59], and paddy soil [27] (Fig. 5).…”

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

“…Polynucleobacter duraquae is also most often found in fresh water samples (and is free-living unlike many host-associated Polynucleobacter species) (Hahn et al, 2016). Similarly, the OTUs annotated as Comamonadaceae MG_12 (placed as within the genera Acidovorax or Limnohabitans) and Bordetella_1 did not correspond to any well characterized bacterial species, but have previously been identified or isolated as unknown bacteria (100% similar) from numerous samples deriving from fresh water (Shaw et al, 2008;Mueller-Spitz et al, 2009;Wu et al, 2012;Elser et al, 2014;Balmonte et al, 2016;Huang et al, 2016) and were also only detected in laboratory samples.…”