Bacteria are an important part of every ecosystem that they inhabit on Earth. Environmental microbiologists usually focus on a few dominant bacterial groups, neglecting less abundant ones, which collectively make up most of the microbial diversity. One of such less-studied phyla is Gemmatimonadota. Currently, the phylum contains only six cultured species. However, data from culture-independent studies indicate that members of Gemmatimonadota are common in diverse habitats. They are abundant in soils, where they seem to be frequently associated with plants and the rhizosphere. Moreover, Gemmatimonadota were found in aquatic environments, such as freshwaters, wastewater treatment plants, biofilms, and sediments. An important discovery was the identification of purple bacterial reaction centers and anoxygenic photosynthesis in this phylum, genes for which were likely acquired via horizontal gene transfer. So far, the capacity for anoxygenic photosynthesis has been described for two cultured species: Gemmatimonas phototrophica and Gemmatimonas groenlandica. Moreover, analyses of metagenome-assembled genomes indicate that it is also common in uncultured lineages of Gemmatimonadota. This review summarizes the current knowledge about this understudied bacterial phylum with an emphasis on its environmental distribution.

• Keywords
• Gemmatimonadetes, Gemmatimonadota, MAGs, anoxygenic photosynthesis, photosynthetic gene cluster,
• Publication type
• Journal Article MeSH
• Review MeSH

Chlorophylls (Chls) are essential cofactors for photosynthesis. One of the least understood steps of Chl biosynthesis is formation of the fifth (E) ring, where the red substrate, magnesium protoporphyrin IX monomethyl ester, is converted to the green product, 3,8-divinyl protochlorophyllide a In oxygenic phototrophs, this reaction is catalyzed by an oxygen-dependent cyclase, consisting of a catalytic subunit (AcsF/CycI) and an auxiliary protein, Ycf54. Deletion of Ycf54 impairs cyclase activity and results in severe Chl deficiency, but its exact role is not clear. Here, we used a Δycf54 mutant of the model cyanobacterium Synechocystis sp. PCC 6803 to generate suppressor mutations that restore normal levels of Chl. Sequencing Δycf54 revertants identified a single D219G amino acid substitution in CycI and frameshifts in slr1916, which encodes a putative esterase. Introduction of these mutations to the original Δycf54 mutant validated the suppressor effect, especially in combination. However, comprehensive analysis of the Δycf54 suppressor strains revealed that the D219G-substituted CycI is only partially active and its accumulation is misregulated, suggesting that Ycf54 controls both the level and activity of CycI. We also show that Slr1916 has Chl dephytylase activity in vitro and its inactivation up-regulates the entire Chl biosynthetic pathway, resulting in improved cyclase activity. Finally, large-scale bioinformatic analysis indicates that our laboratory evolution of Ycf54-independent CycI mimics natural evolution of AcsF in low-light-adapted ecotypes of the oceanic cyanobacteria Prochlorococcus, which lack Ycf54, providing insight into the evolutionary history of the cyclase enzyme.

• Keywords
• chlorophyll, cyanobacteria, cyclase, microevolution, photosynthesis,
• MeSH
• Bacterial Proteins genetics   metabolism   MeSH
• Bacteriochlorophylls biosynthesis   genetics   MeSH
• Gene Deletion * MeSH
• Oxygenases genetics   metabolism   MeSH
• Prochlorococcus genetics   metabolism   MeSH
• Synechocystis genetics   metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Bacterial Proteins MeSH
• Bacteriochlorophylls MeSH
• Oxygenases MeSH

The bacterial phylum Gemmatimonadetes contains members capable of performing bacteriochlorophyll-based phototrophy (chlorophototrophy). However, only one strain of chlorophototrophic Gemmatimonadetes bacteria (CGB) has been isolated to date, hampering our further understanding of their photoheterotrophic lifestyle and the evolution of phototrophy in CGB. By combining a culturomics strategy with a rapid screening technique for chlorophototrophs, we report the isolation of a new member of CGB, Gemmatimonas (G.) groenlandica sp. nov., from the surface water of a stream in the Zackenberg Valley in High Arctic Greenland. Distinct from the microaerophilic G. phototrophica strain AP64T, G. groenlandica strain TET16T is a strictly aerobic anoxygenic phototroph, lacking many oxygen-independent enzymes while possessing an expanded arsenal for coping with oxidative stresses. Its pigment composition and infra-red absorption properties are also different from G. phototrophica, indicating that it possesses a different photosystem apparatus. The complete genome sequence of G. groenlandica reveals unique and conserved features in the photosynthesis gene clusters of CGB. We further analyzed metagenome-assembled genomes of CGB obtained from soil and glacier metagenomes from Northeast Greenland, revealing a wide distribution pattern of CGB beyond the stream water investigated.

• Keywords
• Gemmatimonadetes, MALDI-TOF MS, bacterial isolation, oligotrophic environment, phototrophy,
• Publication type
• Journal Article MeSH

The genus Limnohabitans (Comamonadaceae, Betaproteobacteria) is a common and a highly active component of freshwater bacterioplanktonic communities. To date, the genus has been considered to contain only heterotrophic species. In this study, we detected the photosynthesis genes pufLM and bchY in 28 of 46 strains from three Limnohabitans lineages. The pufM sequences obtained are very closely related to environmental pufM sequences detected in various freshwater habitats, indicating the ubiquity and potential importance of photoheterotrophic Limnohabitans in nature. Additionally, we sequenced and analyzed the genomes of 5 potentially photoheterotrophic Limnohabitans strains, to gain further insights into their phototrophic capacity. The structure of the photosynthesis gene cluster turned out to be highly conserved within the genus Limnohabitans and also among all potentially photosynthetic Betaproteobacteria strains. The expression of photosynthetic complexes was detected in a culture of Limnohabitans planktonicus II-D5T using spectroscopic and pigment analyses. This was further verified by a novel combination of infrared microscopy and fluorescent in situ hybridization.IMPORTANCE The data presented document that the capacity to perform anoxygenic photosynthesis is common among the members of the genus Limnohabitans, indicating that they may have a novel role in freshwater habitats.

• Keywords
• FISH, IR microscopy, Limnohabitans, bacteriochlorophyll, bchY, freshwater Betaproteobacteria, photosynthetic bacteria, pufM,
• MeSH
• Aerobiosis MeSH
• Genes, Bacterial physiology   MeSH
• Bacterial Proteins genetics   metabolism   MeSH
• Comamonadaceae genetics   metabolism   MeSH
• Photosynthesis genetics   MeSH
• Phylogeny MeSH
• Multigene Family physiology   MeSH
• Publication type
• Journal Article MeSH
• Names of Substances
• Bacterial Proteins MeSH

A characteristic feature of the order Rhodobacterales is the presence of a large number of photoautotrophic and photoheterotrophic species containing bacteriochlorophyll. Interestingly, these phototrophic species are phylogenetically mixed with chemotrophs. To better understand the origin of such variability, we sequenced the genomes of three closely related haloalkaliphilic species, differing in their phototrophic capacity and oxygen preference: the photoheterotrophic and facultatively anaerobic bacterium Rhodobaca barguzinensis, aerobic photoheterotroph Roseinatronobacter thiooxidans, and aerobic heterotrophic bacterium Natronohydrobacter thiooxidans. These three haloalcaliphilic species are phylogenetically related and share many common characteristics with the Rhodobacter species, forming together the Rhodobacter-Rhodobaca (RR) group. A comparative genomic analysis showed close homology of photosynthetic proteins and similarity in photosynthesis gene organization among the investigated phototrophic RR species. On the other hand, Rhodobaca barguzinensis and Roseinatronobacter thiooxidans lack an inorganic carbon fixation pathway and outer light-harvesting genes. This documents the reduction of their photosynthetic machinery towards a mostly photoheterotrophic lifestyle. Moreover, both phototrophic species contain 5-aminolevulinate synthase (encoded by the hemA gene) incorporated into their photosynthesis gene clusters, which seems to be a common feature of all aerobic anoxygenic phototrophic Alphaproteobacteria. Interestingly, the chrR-rpoE (sigma24) operon, which is part of singlet oxygen defense in phototrophic species, was found in the heterotrophic strain Natronohydrobacter thiooxidans. This suggests that this organism evolved from a photoheterotrophic ancestor through the loss of its photosynthesis genes. The overall evolution of phototrophy among the haloalkaliphilic members of the RR group is discussed.

• Keywords
• Anoxygenic photosynthesis, Rhodobacteraceae, bacteriochlorophyll, horizontal gene transfer, photosynthesis gene cluster,
• MeSH
• Aerobiosis MeSH
• Bacterial Proteins genetics   MeSH
• Photosynthesis MeSH
• Phototrophic Processes * MeSH
• Phylogeny MeSH
• Genomics MeSH
• Evolution, Molecular * MeSH
• Rhodobacter genetics   MeSH
• Sequence Analysis, DNA methods   MeSH
• Light MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Bacterial Proteins MeSH

UNLABELLED: 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%. IMPORTANCE: Photosynthesis 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.

• MeSH
• Bacteria classification   enzymology   genetics   MeSH
• Bacterial Proteins genetics   MeSH
• DNA, Bacterial chemistry   genetics   MeSH
• DNA Primers MeSH
• Geologic Sediments microbiology   MeSH
• Lakes microbiology   MeSH
• Polymerase Chain Reaction MeSH
• DNA, Ribosomal chemistry   genetics   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Sequence Analysis, DNA MeSH
• Biota * MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• China MeSH
• Names of Substances
• Bacterial Proteins MeSH
• DNA, Bacterial MeSH
• DNA Primers MeSH
• DNA, Ribosomal MeSH
• RNA, Ribosomal, 16S MeSH

In the chlorophyll (Chl) biosynthesis pathway the formation of protochlorophyllide is catalyzed by Mg-protoporphyrin IX methyl ester (MgPME) cyclase. The Ycf54 protein was recently shown to form a complex with another component of the oxidative cyclase, Sll1214 (CycI), and partial inactivation of the ycf54 gene leads to Chl deficiency in cyanobacteria and plants. The exact function of the Ycf54 is not known, however, and further progress depends on construction and characterization of a mutant cyanobacterial strain with a fully inactivated ycf54 gene. Here, we report the complete deletion of the ycf54 gene in the cyanobacterium Synechocystis 6803; the resulting Δycf54 strain accumulates huge concentrations of the cyclase substrate MgPME together with another pigment, which we identified using nuclear magnetic resonance as 3-formyl MgPME. The detection of a small amount (~13%) of Chl in the Δycf54 mutant provides clear evidence that the Ycf54 protein is important, but not essential, for activity of the oxidative cyclase. The greatly reduced formation of protochlorophyllide in the Δycf54 strain provided an opportunity to use (35)S protein labeling combined with 2D electrophoresis to examine the synthesis of all known Chl-binding protein complexes under drastically restricted de novo Chl biosynthesis. We show that although the Δycf54 strain synthesizes very limited amounts of photosystem I and the CP47 and CP43 subunits of photosystem II (PSII), the synthesis of PSII D1 and D2 subunits and their assembly into the reaction centre (RCII) assembly intermediate were not affected. Furthermore, the levels of other Chl complexes such as cytochrome b 6 f and the HliD- Chl synthase remained comparable to wild-type. These data demonstrate that the requirement for de novo Chl molecules differs completely for each Chl-binding protein. Chl traffic and recycling in the cyanobacterial cell as well as the function of Ycf54 are discussed.

• Keywords
• Mg-protoporphyrin IX methylester cyclase, Synechocystis 6803, Ycf54, chlorophyll, photosystem II, protochlorophyllide,
• Publication type
• Journal Article MeSH

The Roseobacter clade represents one of the most important bacterial groups in marine environments. While some of its members are heterotrophs, many Roseobacter clade members contain bacterial photosynthetic reaction centers. We investigated the phylogeny of pufL and pufM genes encoding the L and M subunits of reaction centers using available genomic data and our own cultured species. Interestingly, phylogeny of pufL and pufM genes largely deviated from 16S rRNA-based phylogeny. The sequences split into two clearly distinct clades. While most of the studied species contained pufL and pufM sequences related to those found in Roseobacter litoralis, some of the marine species contained sequences related to the freshwater Rhodobacter species. In addition, genomic data documents that Roseobacter-type centers contain cytochrome c subunits (pufC gene product), whereas Rhodobacter-type centers incorporate PufX proteins. This indicates that the two forms of the reaction centers are not only distinct phylogenetically, but also structurally. The large deviation of pufL and pufM phylogeny from 16S phylogeny indicates multiple horizontal transfers of the puf operon among members of the order Rhodobacterales.

• MeSH
• Bacterial Proteins genetics   metabolism   MeSH
• Phototrophic Processes MeSH
• Phylogeny MeSH
• Molecular Sequence Data MeSH
• Operon * MeSH
• Gene Transfer, Horizontal * MeSH
• Roseobacter classification   genetics   metabolism   MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• Bacterial Proteins MeSH

Photosynthetic bacteria emerged on Earth more than 3 Gyr ago. To date, despite a long evolutionary history, species containing (bacterio)chlorophyll-based reaction centers have been reported in only 6 out of more than 30 formally described bacterial phyla: Cyanobacteria, Proteobacteria, Chlorobi, Chloroflexi, Firmicutes, and Acidobacteria. Here we describe a bacteriochlorophyll a-producing isolate AP64 that belongs to the poorly characterized phylum Gemmatimonadetes. This red-pigmented semiaerobic strain was isolated from a freshwater lake in the western Gobi Desert. It contains fully functional type 2 (pheophytin-quinone) photosynthetic reaction centers but does not assimilate inorganic carbon, suggesting that it performs a photoheterotrophic lifestyle. Full genome sequencing revealed the presence of a 42.3-kb-long photosynthesis gene cluster (PGC) in its genome. The organization and phylogeny of its photosynthesis genes suggests an ancient acquisition of PGC via horizontal transfer from purple phototrophic bacteria. The data presented here document that Gemmatimonadetes is the seventh bacterial phylum containing (bacterio)chlorophyll-based phototrophic species. To our knowledge, these data provide the first evidence that (bacterio)chlorophyll-based phototrophy can be transferred between distant bacterial phyla, providing new insights into the evolution of bacterial photosynthesis.

• Keywords
• aerobic photoheterotroph, anoxygenic photosynthesis, bacterial pigments, fluorescence imaging system, horizontal gene transfer,
• MeSH
• Bacteria cytology   genetics   metabolism   MeSH
• Species Specificity MeSH
• Microscopy, Fluorescence MeSH
• Fluorometry MeSH
• Photosystem II Protein Complex genetics   metabolism   MeSH
• Phylogeny * MeSH
• Lakes microbiology   MeSH
• Models, Genetic MeSH
• Molecular Sequence Data MeSH
• Likelihood Functions MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Base Sequence MeSH
• Sequence Analysis, DNA MeSH
• Cluster Analysis MeSH
• Spectrum Analysis MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• China MeSH
• Names of Substances
• Photosystem II Protein Complex MeSH
• RNA, Ribosomal, 16S MeSH