New Light on Aerobic Anoxygenic Phototrophs

Do carotenoids protect phytodetritus-associated bacteria from oxidative stress?

This study focused on how carotenoid pigments in bacteria attached to phytoplankton protect them from singlet oxygen produced by phytoplankton during senescence, specifically under illumination of the diatom Thalassiosira sp. Its effect was analyzed on bacterial membrane structure (photooxidation of bacterial membrane lipids such as mono-unsaturated fatty acids (MUFAs) and on DNA repair system in two bacterial species, non-pigmented Pseudomonas stutzeri and pigmented Dinoroseobacter shibae. In P. stutzeri cells, 1O₂ transferred from phytodetritus was not completely scavenged by bacterial membranous MUFAs and reached the cytoplasm, allowing both 1O₂ and UV radiation to cause a rapid response of DNA repair systems. In D. shibae, scavenging by bacterial membrane MUFAs and quenching by spheroidenone allowed only a small fraction of 1O₂ to reach the cytoplasm, as shown by a delayed and lower repair system activation. The fact that Rhodobacteriales is the dominant order in bacterioplankton communities associated with algal blooms could thus be partly due to the protective effect of its constituent carotenoids against 1O₂- and UV-induced damage.

Microbial occurrence and symbiont detection in a global sample of lichen metagenomes

In lichen research, metagenomes are increasingly being used for evaluating symbiont composition and metabolic potential, but the overall content and limitations of these metagenomes have not been assessed. We reassembled over 400 publicly available metagenomes, generated metagenome-assembled genomes (MAGs), constructed phylogenomic trees, and mapped MAG occurrence and frequency across the data set. Ninety-seven percent of the 1,000 recovered MAGs were bacterial or the fungal symbiont that provides most cellular mass. Our mapping of recovered MAGs provides the most detailed survey to date of bacteria in lichens and shows that 4 family-level lineages from 2 phyla accounted for as many bacterial occurrences in lichens as all other 71 families from 16 phyla combined. Annotation of highly complete bacterial, fungal, and algal MAGs reveals functional profiles that suggest interdigitated vitamin prototrophies and auxotrophies, with most lichen fungi auxotrophic for biotin, most bacteria auxotrophic for thiamine and the few annotated algae with partial or complete pathways for both, suggesting a novel dimension of microbial cross-feeding in lichen symbioses. Contrary to longstanding hypotheses, we found no annotations consistent with nitrogen fixation in bacteria other than known cyanobacterial symbionts. Core lichen symbionts such as algae were recovered as MAGs in only a fraction of the lichen symbioses in which they are known to occur. However, the presence of these and other microbes could be detected at high frequency using small subunit rRNA analysis, including in many lichens in which they are not otherwise recognized to occur. The rate of MAG recovery correlates with sequencing depth, but is almost certainly influenced by biological attributes of organisms that affect the likelihood of DNA extraction, sequencing and successful assembly, including cellular abundance, ploidy and strain co-occurrence. Our results suggest that, though metagenomes are a powerful tool for surveying microbial occurrence, they are of limited use in assessing absence, and their interpretation should be guided by an awareness of the interacting effects of microbial community complexity and sequencing depth.

Novel aerobic anoxygenic phototrophic bacterium Jannaschia pagri sp. nov., isolated from seawater around a fish farm

The genus Jannaschia is one of the representatives of aerobic anoxygenic phototrophic (AAP) bacteria, which is a strictly aerobic bacterium, producing a photosynthetic pigment bacteriochlorophyll (BChl) a. However, a part of the genus Jannaschia members have not been confirmed the photosynthetic ability. The partly presence of the ability in the genus Jannaschia could suggest the complexity of evolutionary history for anoxygenic photosynthesis in the genus, which is expected as gene loss and/or horizontal gene transfer. Here a novel AAP bacterium designated as strain AI_62T (= DSM 115720 T = NBRC 115938 T), was isolated from coastal seawater around a fish farm in the Uwa Sea, Japan. Its closest relatives were identified as Jannaschia seohaensis SMK-146 T (95.6% identity) and J. formosa 12N15T (94.6% identity), which have been reported to produce BChl a. The genomic characteristic of strain AI_62T clearly showed the possession of the anoxygenic photosynthesis related gene sets. This could be a useful model organism to approach the evolutionary mystery of anoxygenic photosynthesis in the genus Jannaschia. Based on a comprehensive consideration of both phylogenetic and phenotypic characteristics, we propose the classification of a novel species within the genus Jannaschia, designated as Jannaschia pagri sp. nov. The type strain for this newly proposed species is AI_62T (= DSM 115720 T = NBRC 115938 T).

Multifaceted photoreceptor compositions in dual phototrophic systems - A genomic analysis

For microbes and their hosts, sensing of external cues is essential for their survival. For example, in the case of plant associated microbes, the light absorbing pigment composition of the plant as well as the ambient light conditions determine the well-being of the microbe. In addition to light sensing, some microbes can utilize xanthorhodopsin based proton pumps and bacterial photosynthetic complexes that work in parallel for energy production. They are called dual phototrophic systems. Light sensing requirements in these type of systems are obviously demanding. In nature, the photosensing machinery follows mainly the same composition in all organisms. However, the specific role of each photosensor in specific light conditions is elusive. In this study, we provide an overall picture of photosensors present in dual phototrophic systems. We compare the genomes of the photosensor proteins from dual phototrophs to those from similar microbes with "single" phototrophicity or microbes without phototrophicity. We find that the dual phototrophic bacteria obtain a larger variety of photosensors than their light inactive counterparts. Their rich domain composition and functional repertoire remains similar across all microbial photosensors. Our study calls further investigations of this particular group of bacteria. This includes protein specific biophysical characterization in vitro, microbiological studies, as well as clarification of the ecological meaning of their host microbial interactions.

Genomic basis for the unique phenotype of the alkaliphilic purple nonsulfur bacterium Rhodobaca bogoriensis

Although several species of purple sulfur bacteria inhabit soda lakes, Rhodobaca bogoriensis is the first purple nonsulfur bacterium cultured from such highly alkaline environments. Rhodobaca bogoriensis strain LBB1T was isolated from Lake Bogoria, a soda lake in the African Rift Valley. The phenotype of Rhodobaca bogoriensis is unique among purple bacteria; the organism is alkaliphilic but not halophilic, produces carotenoids absent from other purple nonsulfur bacteria, and is unable to grow autotrophically or fix molecular nitrogen. Here we analyze the draft genome sequence of Rhodobaca bogoriensis to gain further insight into the biology of this extremophilic purple bacterium. The strain LBB1T genome consists of 3.91 Mbp with no plasmids. The genome sequence supports the defining characteristics of strain LBB1T, including its (1) production of a light-harvesting 1-reaction center (LH1-RC) complex but lack of a peripheral (LH2) complex, (2) ability to synthesize unusual carotenoids, (3) capacity for both phototrophic (anoxic/light) and chemotrophic (oxic/dark) energy metabolisms, (4) utilization of a wide variety of organic compounds (including acetate in the absence of a glyoxylate cycle), (5) ability to oxidize both sulfide and thiosulfate despite lacking the capacity for autotrophic growth, and (6) absence of a functional nitrogen-fixation system for diazotrophic growth. The assortment of properties in Rhodobaca bogoriensis has no precedent among phototrophic purple bacteria, and the results are discussed in relation to the organism's soda lake habitat and evolutionary history.

Prosthecate aerobic anoxygenic phototrophs Photocaulis sulfatitolerans gen. nov. sp. nov. and Photocaulis rubescens sp. nov. isolated from alpine meromictic lakes in British Columbia, Canada

Seven Gram-negative flagellated and subsequent prosthecate bacteria were isolated from meromictic Mahoney Lake and Blue Lake in British Columbia, Canada. Each became pink-red after 1-2 weeks of incubation, containing bacteriochlorophyll a incorporated into light harvesting and reaction center pigment-protein complexes. They did not grow anaerobically under illuminated conditions, supporting their identification as obligate aerobic anoxygenic phototrophs (AAP). All isolates preferred high salinity and BL14^T tolerated up to 6.5% NaCl or 16.0% Na₂SO₄. In addition to phenotypic differences, analysis of 16S rRNA gene sequences found both strains BL14^T and ML37^T were related to Alkalicaulis satelles, G-192^T by 98.41 and 98.84%, respectively, and distantly associated to members of the non-phototrophic genus Glycocaulis profundi, ZYF765^T (95.59 and 95.36%, respectively) within the newly recognized Maricaulales order of α-Proteobacteria. BL14^T and ML37^T contained photosynthetic operons of 46,143 and 46,315 bp, where genes of BL14^T were uniquely split into two distal operons. Furthermore, A. satelles was not originally published as an AAP, but was also found in this work to contain a similar 45,131 bp fragment. The distinct morphological features, physiological traits and genomic analysis including average nucleotide identity and digital DNA:DNA hybridization of circularized genomes supported the proposal of new genus and species Photocaulis sulfatitolerans gen. nov. sp. nov., type strain BL14^T and Photocaulis rubescens sp. nov. type strain ML37^T.

Neotabrizicola shimadae gen. nov., sp. nov., an aerobic anoxygenic phototrophic bacterium harbouring photosynthetic genes in the family Rhodobacteraceae, isolated from a terrestrial hot spring

A bacteriochlorophyll-containing bacterium, designated as strain N10^T, was isolated from a terrestrial hot spring in Nagano Prefecture, Japan. Gram-stain-negative, oxidase- and catalase-positive and ovoid to rod-shaped cells showed the features of aerobic anoxygenic phototrophic bacteria, i.e., strain N10^T synthesised bacteriochlorophylls under aerobic conditions and could not grow anaerobically even under illumination. Genome analysis found genes for bacteriochlorophyll and carotenoid biosynthesis, light-harvesting complexes and type-2 photosynthetic reaction centre in the chromosome. Phylogenetic analyses based on the 16S rRNA gene sequence and 92 core proteins revealed that strain N10^T was located in a distinct lineage near the type species of the genera Tabrizicola and Xinfangfangia and some species in the genus Rhodobacter (e.g., Rhodobacter blasticus). Strain N10^T shared < 97.1% 16S rRNA gene sequence identity with those species in the family Rhodobacteraceae. The digital DNA-DNA hybridisation, average nucleotide identity and average amino acid identity values with the relatives, Tabrizicola aquatica RCRI19^T (an aerobic anoxygenic phototrophic bacterium), Xinfangfangia soli ZQBW^T and R. blasticus ATCC 33485^T were 19.9-20.7%, 78.2-79.1% and 69.1-70.1%, respectively. Based on the phenotypic features, major fatty acid and polar lipid compositions, genome sequence and phylogenetic position, a novel genus and species are proposed for strain N10^T, to be named Neotabrizicola shimadae (= JCM 34381^T = DSM 112087T). Strain N10^T which is phylogenetically located among aerobic anoxygenic phototrophic bacteria (Tabrizicola), bacteriochlorophyll-deficient bacteria (Xinfangfangia) and anaerobic anoxygenic phototrophic bacteria (Rhodobacter) has great potential to promote studies on the evolution of photosynthesis in Rhodobacteraceae.

Phylum Gemmatimonadota and Its Role in the Environment

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.

Soil Chemistry and Nutrients Influence the Distribution of Aerobic Anoxygenic Phototrophic Bacteria and Eukaryotic Phototrophic Microorganisms of Physical Soil Crusts at Different Elevations on the Tibetan Plateau

Photosynthetic microorganisms are widely distributed in the soil and play an important role in plant-free soil crusts. However, the distribution and environmental drivers of phototrophic microbial communities in physical soil crusts, where the abundance of cyanobacteria is low, are scarcely understood. Here, we performed high-throughput sequencing of pufM and 18S rRNA genes in soil crusts at different elevations on the Tibetan Plateau and used the data combined with environmental variables to analyze the diversity and structure of phototrophic microbial communities. We found that the dominant taxa of aerobic anoxygenic phototrophic bacteria (AAPB) and eukaryotic phototrophic microorganisms (EPM) were shown to shift with elevation. The phototrophic microbial diversity showed a single-peak pattern, with the lowest diversity of AAPB and highest diversity of EPM at middle elevations. Moreover, the elevation and soil property determined the phototrophic microbial community. Soil salts, especially Cl^-, were the most important for AAPB. Likewise, soil nutrients, especially carbon, were the most important for EPM. The relationship between high-abundance taxa and environmental variables showed that Rhizobiales was significantly negatively correlated with salt ions and positively correlated with chlorophyll. Rhodobacterales showed the strongest and significant positive associations with Cl^-. Chlorophyceae and Bacillariophyceae were positively correlated with CO₃^2-. These results indicated that salinity and soil nutrients affected the diversity and structure of microbial communities. This study contributes to our understanding of the diversity, composition, and structure of photosynthetic microorganisms in physical soil crusts and helps in developing new approaches for controlling desertification and salinization and improving the desert ecological environment.

Microbial Community Composition during a Bloom of Purple Bacteria in Intertidal Sediments in Vigo (Northwest Spain)

In summer 2019, a large, bright pink microbial mat was visible on top of macroalgal deposits in muddy sediments of an urban beach (Playa do Adro, Vigo). In order to characterize the dominant organisms in these colored mats, results from microscopic observations, photosynthetic pigments, and molecular analysis were gathered. Light microscopy examination revealed pinkish microbial aggregates with minor contributions of larger protists and cyanobacteria. High-performance liquid chromatography (HPLC) pigment analysis documented the dominance of bacteriochlorophyll a and carotenoids whose spectra were compatible with those described in photosynthetic purple bacteria. 16S rRNA gene amplicon sequencing confirmed that the vast majority of reads belonged to Proteobacteria (73.5%), and among them, nearly 88% of those reads belonged to purple sulfur bacteria (Gammaproteobacteria). A single family, Chromatiaceae, constituted the bulk of this assemblage, including the genera Thiohalocapsa (32%), Marichromatium (12.5%), Phaeochromatium (5%), and Halocromatium (2%) as main contributors. Nonetheless, a considerable number of sequences could not be assigned to a particular genus, stressing the large biological diversity in these microbial mats and the potential presence of novel taxa of purple sulfur bacteria. IMPORTANCE Urban beaches are valuable recreational areas particularly vulnerable to human disturbance. In these areas, the intertidal sediments harbor a diverse community of microorganisms, including virus, bacteria, fungi, and protozoa. In this sense, pollution events can introduce pathogenic allochthonous microbes which may constitute a human health risk. Visual and sensory observations, such as a weird color or bad smell, are usually appreciated as a warning by beachgoers and authorities, as indeed was the case at do Adro beach in 2019. The observed proliferation seems to be common in summertime, but its dimension alerted beachgoers and media. The obtained results allowed for the identification of purple sulfur bacteria as responsible for the pink-violet top layer staining the intertidal zone. These blooms have never been associated with public health risks. Beyond solving the sanitary concern, other important findings were its diversity and large proportion of novel taxa, illustrating the complexity of these ecosystems.

Structure elucidation of the novel carotenoid gemmatoxanthin from the photosynthetic complex of Gemmatimonas phototrophica AP64

Gemmatimonas phototrophica AP64 is the first phototrophic representative of the bacterial phylum Gemmatimonadetes. The cells contain photosynthetic complexes with bacteriochlorophyll a as the main light-harvesting pigment and an unknown carotenoid with a single broad absorption band at 490 nm in methanol. The carotenoid was extracted from isolated photosynthetic complexes, and purified by liquid chromatography. A combination of nuclear magnetic resonance (1H NMR, COSY, 1H-13C HSQC, 1H-13C HMBC, J-resolved, and ROESY), high-resolution mass spectroscopy, Fourier-transformed infra-red, and Raman spectroscopy was used to determine its chemical structure. The novel linear carotenoid, that we have named gemmatoxanthin, contains 11 conjugated double bonds and is further substituted by methoxy, carboxyl and aldehyde groups. Its IUPAC-IUBMB semi-systematic name is 1'-Methoxy-19'-oxo-3',4'-didehydro-7,8,1',2'-tetrahydro- Ψ, Ψ carotene-16-oic acid. To our best knowledge, the presence of the carboxyl, methoxy and aldehyde groups on a linear C40 carotenoid backbone is reported here for the first time.

Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030^T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C_18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO₂-fixation pathways were found.

Carotenoids produced by the deep-sea bacterium Erythrobacter citreus LAMA 915: detection and proposal of their biosynthetic pathway

Technologies based on synthetic biology to produce bacterial natural carotenoids depend on information regarding their biosynthesis. Although the biosynthetic pathway of common carotenoids is known, there are carotenoids whose pathways are not completely described. This work aimed to mine the genome of the deep-sea bacterium Erythrobacter citreus LAMA 915, an uncommon bacterium that forms yellow colonies under cultivation. This work further explores the potential application of the carotenoids found and low-cost substrates for bacterial growth. A combined approach of genome mining and untargeted metabolomics analysis was applied. The carotenoid erythroxanthin sulfate was detected in E. citreus LAMA 915 cell extract. A proposal for carotenoid biosynthesis by this bacterium is provided, involving the genes crtBIYZWG. These are responsible for the biosynthesis of carotenoids from the zeaxanthin pathway and their 2,2'-hydroxylated derivatives. E. citreus LAMA 915 extracts showed antioxidant and sun protection effects. Based on the high content of proteases and lipases, it was possible to rationally select substrates for bacterial growth, with residual oil from fish processing the best low-cost substrate selected. This work advances in the understanding of carotenoid biosynthesis and provides a genetic basis that can be further explored as a biotechnological route for carotenoid production.

Aerophototrophica crusticola gen. nov., sp. nov., isolated from desert biocrusts

A pink-pigmented, Gram-stain-negative, rod-shaped, strictly aerobic bacterial strain MIMtkB3^T, was isolated from moss crusts in Hunshandake desert of China. Cells grew at 15-45 °C (optimum of 28 °C), at pH of 6.0-8.5 (optimum of 7.0) and with 0-1.0 % (w/v) NaCl (optimum of 0 %). The strain could biosynthesize the green-coloured pigment bacteriochlorophyll a (BChl a). The respiratory quinone was ubiquinone Q-10, while C_18 : 1 ω7c and C_18 : 1 2OH were the major fatty acids. Phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an unidentified aminophospholipid, one unidentified phospholipid, three unidentified glycolipid and one unidentified lipid were the major polar lipids. Strain MIMtkB3^T was most closely related to Oleisolibacter albus NAU-10^T, Niveispirillum fermenti CC-LY736^T, and Rhodocista centenaria SW of the family Rhodospirillaceae with 16S rRNA gene similarities of 93.09, 92.02 and 91.73%, respectively. The genomic DNA G+C content calculated on complete genome sequencing was 69.3 mol%. The average nucleotide identity between strain MIMtkB3^T and its closely related type strains in Rhodospirillaceae was below 77.96 % and digital DNA-DNA hybridization lower than 24.70 %. Full light utilization pathway of aerobic anoxygenic phototrophic bacteria was identified in the genome. Based on phenotypic, chemotaxonomic and phylogenetic characteristics, strain MIMtkB3^T represents a novel genus of the family Rhodospirillaceae, for which the name Aerophototrophica crusticola gen. nov., sp. nov. is proposed. The type strain is MIMtkB3^T (=KCTC 42633^T=MCCC 1K00570^T).

Simultaneous Presence of Bacteriochlorophyll and Xanthorhodopsin Genes in a Freshwater Bacterium

Photoheterotrophic bacteria represent an important part of aquatic microbial communities. There exist two fundamentally different light-harvesting systems: bacteriochlorophyll-containing reaction centers or rhodopsins. Here, we report a photoheterotrophic Sphingomonas strain isolated from an oligotrophic lake, which contains complete sets of genes for both rhodopsin-based and bacteriochlorophyll-based phototrophy. Interestingly, the identified genes were not expressed when cultured in liquid organic media. Using reverse transcription quantitative PCR (RT-qPCR), RNA sequencing, and bacteriochlorophyll a quantification, we document that bacteriochlorophyll synthesis was repressed by high concentrations of glucose or galactose in the medium. Coactivation of photosynthesis genes together with genes for TonB-dependent transporters suggests the utilization of light energy for nutrient import. The photosynthetic units were formed by ring-shaped light-harvesting complex 1 and reaction centers with bacteriochlorophyll a and spirilloxanthin as the main light-harvesting pigments. The identified rhodopsin gene belonged to the xanthorhodopsin family, but it lacks salinixanthin antenna. In contrast to bacteriochlorophyll, the expression of xanthorhodopsin remained minimal under all experimental conditions tested. Since the gene was found in the same operon as a histidine kinase, we propose that it might serve as a light sensor. Our results document that photoheterotrophic Sphingomonas bacteria use the energy of light under carbon-limited conditions, while under carbon-replete conditions, they cover all their metabolic needs through oxidative phosphorylation.IMPORTANCE Phototrophic organisms are key components of many natural environments. There exist two main phototrophic groups: species that collect light energy using various kinds of (bacterio)chlorophylls and species that utilize rhodopsins. Here, we present a freshwater bacterium Sphingomonas sp. strain AAP5 which contains genes for both light-harvesting systems. We show that bacteriochlorophyll-based reaction centers are repressed by light and/or glucose. On the other hand, the rhodopsin gene was not expressed significantly under any of the experimental conditions. This may indicate that rhodopsin in Sphingomonas may have other functions not linked to bioenergetics.

Photosynthetic complexes and light-dependant electron transport chain in the aerobic anoxygenic phototroph Roseicyclus mahoneyensis and its spontaneous mutants

Spontaneous photosynthetic mutants of the aerobic anoxygenic phototrophic bacterium Roseicyclus mahoneyensis, strain ML6 have been identified based on phenotypic differences and spectrophotometric analysis. ML6 contains a reaction centre (RC) with absorption peaks at 755, 800, and 870 nm, light harvesting (LH) complex 1 at 870 nm, and monomodal LH2 at 805 nm; the mutant ML6(B) has only the LH2; ML6(DB) has also lost the LH1; in ML6(BN9O), the LH2 is absent and concentrations of LH1 and RC are much lower than in the wild type. RCs were isolated and purified from ML6 and ML6(BN9O); LH1-RC from ML6; and LH2 from ML6, ML6(B), and ML6(DB). All protein subunits composing the complexes were found to be of typical size. Flash-induced difference spectra revealed ML6 has a fully functional photosynthetic apparatus under aerobic and microaerophilic conditions, and as is typical for AAP, there is no photosynthetic activity anaerobically. ML6(BN9O), while also functional photosynthetically aerobically, showed lower rates due to the lack of LH2 and decreased concentrations of LH1 and RC. ML6(B) and ML6(DB) showed no photoinduced electron transport. Action spectra of light-mediated reactions were also performed on ML6 and ML6(BN9O) to reveal that the majority of carotenoids are not involved in light harvesting. Finally, redox titrations were carried out on membranes of ML6 and ML6(BN9O) to confirm that midpoint redox potentials of the Q_A, RC-bound cytochrome, and P⁺ were similar in both strains. Q_A midpoint potential is + 65 mV, cytochrome is + 245 mV, and P⁺ is + 430 mV.

Energetic Basis of Microbial Growth and Persistence in Desert Ecosystems

Microbial life is surprisingly abundant and diverse in global desert ecosystems. In these environments, microorganisms endure a multitude of physicochemical stresses, including low water potential, carbon and nitrogen starvation, and extreme temperatures. In this review, we summarize our current understanding of the energetic mechanisms and trophic dynamics that underpin microbial function in desert ecosystems. Accumulating evidence suggests that dormancy is a common strategy that facilitates microbial survival in response to water and carbon limitation. Whereas photoautotrophs are restricted to specific niches in extreme deserts, metabolically versatile heterotrophs persist even in the hyper-arid topsoils of the Atacama Desert and Antarctica. At least three distinct strategies appear to allow such microorganisms to conserve energy in these oligotrophic environments: degradation of organic energy reserves, rhodopsin- and bacteriochlorophyll-dependent light harvesting, and oxidation of the atmospheric trace gases hydrogen and carbon monoxide. In turn, these principles are relevant for understanding the composition, functionality, and resilience of desert ecosystems, as well as predicting responses to the growing problem of desertification.

Extreme Environments and High-Level Bacterial Tellurite Resistance

Bacteria have long been known to possess resistance to the highly toxic oxyanion tellurite, most commonly though reduction to elemental tellurium. However, the majority of research has focused on the impact of this compound on microbes, namely E. coli, which have a very low level of resistance. Very little has been done regarding bacteria on the other end of the spectrum, with three to four orders of magnitude greater resistance than E. coli. With more focus on ecologically-friendly methods of pollutant removal, the use of bacteria for tellurite remediation, and possibly recovery, further highlights the importance of better understanding the effect on microbes, and approaches for resistance/reduction. The goal of this review is to compile current research on bacterial tellurite resistance, with a focus on high-level resistance by bacteria inhabiting extreme environments.

Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria

A strictly aerobic, bacteriochlorophyll a-containing betaproteobacterium, designated strain W35^T, was isolated from a biofilm sampled at Tama River in Japan. The non-motile and rod-shaped cells formed pink-beige pigmented colonies on agar plates containing organic compounds, and showed an in vivo absorption maximum at 871 nm in the near-infrared region, typical for the presence of bacteriochlorophyll a. The new bacterial strain is Gram-negative, and oxidase- and catalase-positive. Phylogenetic analysis based on 16S rRNA gene sequence showed that strain W35^T was closely related to species in the genus Aquabacterium. The closest phylogenetic relatives of strain W35^T were Aquabacterium commune B8^T (97.9 % sequence similarity), Aquabacterium citratiphilum B4^T (97.2 %) and Aquabacterium limnoticum ABP-4^T (97.0 %). The major cellular fatty acids were C_{16  :  1}ω7c (50.4 %), C_{16  :  0} (22.7 %), summed feature 8 (C_{18  :  1}ω7c/C_{18  :  1}ω6c; 9.7 %), C_{18  :  3}ω6c (5.5 %), C_{12  :  0} (5.3 %) and C_{10  :  0} 3OH (2.7 %). The respiratory quinone was ubiquinone-8. Predominant polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The G+C content of the genomic DNA was 70.4 mol% (genome data) and 71.4 mol% (HPLC). The genome size of strain W35^T is 6.1 Mbp and average nucleotide identity analysis indicated genome similarities of strain W35^T and related Aquabacterium type strains to be 78-79 %. The results of polyphasic comparisons showed that strain W35^T was clearly distinguishable from other members of the genus Aquabacterium. Therefore, we propose a new species in the genus Aquabacterium, namely, Aquabacterium pictum sp. nov. The type strain is W35^T (=DSM 106757^T=NBRC 111963^T). The description of the genus Aquabacterium is also emended.

Characteristics and Evolutionary Analysis of Photosynthetic Gene Clusters on Extrachromosomal Replicons: from Streamlined Plasmids to Chromids

Aerobic anoxygenic photoheterotrophic bacteria (AAPB) represent a bacteriochlorophyll a-containing functional group. Substantial evidence indicates that highly conserved photosynthetic gene clusters (PGCs) of AAPB can be transferred between species, genera, and even phyla. Furthermore, analysis of recently discovered PGCs carried by extrachromosomal replicons (exPGCs) suggests that extrachromosomal replicons (ECRs) play an important role in the transfer of PGCs. In this study, 13 Roseobacter clade genomes from seven genera that harbored exPGCs were used to analyze the characteristics and evolution of PGCs. The identification of plasmid-like and chromid-like ECRs among PGC-containing ECRs revealed two different functions: the spread of PGCs among strains and the maintenance of PGCs within genomes. Phylogenetic analyses indicated two independent origins of exPGCs, corresponding to PufC-containing and PufX-containing puf operons. Furthermore, the two different types of operons were observed within different strains of the same Tateyamaria and Jannaschia genera. The PufC-containing and PufX-containing operons were also differentially carried by chromosomes and ECRs in the strains, respectively, which provided clear evidence for ECR-mediated PGC transfer. Multiple recombination events of exPGCs were also observed, wherein the majority of exPGCs were inserted by replication modules at the same genomic positions. However, the exPGCs of the Jannaschia strains comprised superoperons without evidence of insertion and therefore likely represent an initial evolutionary stage where the PGC was translocated from chromosomes to ECRs without further combinations. Finally, a scenario of PGC gain and loss is proposed that specifically focuses on ECR-mediated exPGC transfer to explain the evolution and patchy distribution of AAPB within the Roseobacter clade.IMPORTANCE The evolution of photosynthesis was a significant event during the diversification of biological life. Aerobic anoxygenic photoheterotrophic bacteria (AAPB) share physiological characteristics with chemoheterotrophs and represent an important group associated with bacteriochlorophyll-dependent phototrophy in the environment. Here, characterization and evolutionary analyses were conducted for 13 bacterial strains that contained photosynthetic gene clusters (PGCs) carried by extrachromosomal replicons (ECRs) to shed light on the evolution of chlorophototrophy in bacteria. This report advances our understanding of the importance of ECRs in the transfer of PGCs within marine photoheterotrophic bacteria.

Microbial distribution and turnover in Antarctic microbial mats highlight the relevance of heterotrophic bacteria in low-nutrient environments

Maritime Antarctica has shown the highest increase in temperature in the Southern Hemisphere. Under this scenario, biogeochemical cycles may be altered, resulting in rapid environmental change for Antarctic biota. Microbes that drive biogeochemical cycles often form biofilms or microbial mats in continental meltwater environments. Limnetic microbial mats from the Fildes Peninsula were studied using high-throughput 16S rRNA gene sequencing. Mat samples were collected from 15 meltwater stream sites, comprising a natural gradient from ultraoligotrophic glacier flows to meltwater streams exposed to anthropogenic activities. Our analyses show that microbial community structure differences between mats are explained by environmental NH4+, NO3-, DIN, soluble reactive silicon and conductivity. Microbial mats living under ultraoligotrophic meltwater conditions did not exhibit a dominance of cyanobacterial photoautotrophs, as has been documented for other Antarctic limnetic microbial mats. Instead, ultraoligotrophic mat communities were characterized by the presence of microbes recognized as heterotrophs and photoheterotrophs. This suggests that microbial capabilities for recycling organic matter may be a key factor to dwell in ultra-low nutrient conditions. Our analyses show that phylotype level assemblages exhibit coupled distribution patterns in environmental oligotrophic inland waters. The evaluation of these microbes suggests the relevance of reproductive and structural strategies to pioneer these psychrophilic ultraoligotrophic environments.

Role of Caulobacter Cell Surface Structures in Colonization of the Air-Liquid Interface

In aquatic environments, Caulobacter spp. can be found at the boundary between liquid and air known as the neuston. I report an approach to study temporal features of Caulobacter crescentus colonization and pellicle biofilm development at the air-liquid interface and have defined the role of cell surface structures in this process. At this interface, C. crescentus initially forms a monolayer of cells bearing a surface adhesin known as the holdfast. When excised from the liquid surface, this monolayer strongly adheres to glass. The monolayer subsequently develops into a three-dimensional structure that is highly enriched in clusters of stalked cells known as rosettes. As this pellicle film matures, it becomes more cohesive and less adherent to a glass surface. A mutant strain lacking a flagellum does not efficiently reach the surface, and strains lacking type IV pili exhibit defects in organization of the three-dimensional pellicle. Strains unable to synthesize the holdfast fail to accumulate at the boundary between air and liquid and do not form a pellicle. Phase-contrast images support a model whereby the holdfast functions to trap C. crescentus cells at the air-liquid boundary. Unlike the holdfast, neither the flagellum nor type IV pili are required for C. crescentus to partition to the air-liquid interface. While it is well established that the holdfast enables adherence to solid surfaces, this study provides evidence that the holdfast has physicochemical properties that allow partitioning of nonmotile mother cells to the air-liquid interface and facilitate colonization of this microenvironment.IMPORTANCE In aquatic environments, the boundary at the air interface is often highly enriched with nutrients and oxygen. Colonization of this niche likely confers a significant fitness advantage in many cases. This study provides evidence that the cell surface adhesin known as a holdfast enables Caulobacter crescentus to partition to and colonize the air-liquid interface. Additional surface structures, including the flagellum and type IV pili, are important determinants of colonization and biofilm formation at this boundary. Considering that holdfast-like adhesins are broadly conserved in Caulobacter spp. and other members of the diverse class Alphaproteobacteria, these surface structures may function broadly to facilitate colonization of air-liquid boundaries in a range of ecological contexts, including freshwater, marine, and soil ecosystems.

Aerobic Anoxygenic Phototrophic Bacteria Promote the Development of Biological Soil Crusts

Chlorophyll-containing oxygenic photoautotrophs have been well known to play a fundamental role in the development of biological soil crusts (BSCs) by harvesting solar radiations and providing fixed carbon to the BSCs ecosystems. Although the same functions can be theoretically fulfilled by the widespread bacteriochlorophyll-harboring aerobic anoxygenic phototrophic bacteria (AAnPB), whether AAnPB play a role in the formation of BSCs and how important they are to this process remain largely unknown. To address these questions, we set up a microcosm system with surface sands of the Hopq desert in northern China and observed the significant effects of near-infrared illumination on the development of BSCs. Compared to near-infrared or red light alone, the combined use of near-infrared and red lights for illumination greatly increased the thickness of BSCs, their organic matter contents and the microalgae abundance by 24.0, 103.7, and 1447.6%, respectively. These changes were attributed to the increasing abundance of AAnPB that can absorb near-infrared radiations. Our data suggest that AAnPB is a long-overlooked driver in promoting the development of BSCs in drylands.

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales

The order Sphingomonadales is a taxon of bacteria with a variety of physiological features and carotenoid pigments. Some of the coloured strains within this order are known to be aerobic anoxygenic phototrophs that contain characteristic photosynthesis gene clusters (PGCs). Previous work has shown that majority of the ORFs putatively involved in the biosynthesis of C₄₀ carotenoids are located outside the PGCs in these strains. The main purpose of this study was to understand the genetic basis for the various colour/carotenoid phenotypes of the strains of Sphingomonadales. Comparative analyses of the genomes of 41 strains of this order revealed that there were different patterns of clustering of carotenoid biosynthesis (crt) ORFs, with four ORF clusters being the most common. The analyses also revealed that co-occurrence of crtY and crtI is an evolutionarily conserved feature in Sphingomonadales and other carotenogenic bacteria. The comparisons facilitated the categorisation of bacteria of this order into four groups based on the presence of different crt ORFs. Yellow coloured strains most likely accumulate nostoxanthin, and contain six ORFs (group I: crtE, crtB, crtI, crtY, crtZ, crtG). Orange coloured strains may produce adonixanthin, astaxanthin, canthaxanthin and erythroxanthin, and contain seven ORFs (group II: crtE, crtB, crtI, crtY, crtZ, crtG, crtW). Red coloured strains may accumulate astaxanthin, and contain six ORFs (group III: crtE, crtB, crtI, crtY, crtZ, crtW). Non-pigmented strains may contain a smaller subset of crt ORFs, and thus fail to produce any carotenoids (group IV). The functions of many of these ORFs remain to be characterised.

Biogeographic patterns of aerobic anoxygenic phototrophic bacteria reveal an ecological consistency of phylogenetic clades in different oceanic biomes

In marine environments, aerobic anoxygenic phototrophic (AAP) bacterial assemblages vary in space and along environmental gradients but the factors shaping their diversity and distribution at different taxonomic levels remain poorly identified. Using sets of sequences encoding the M sub-unit of the photosynthetic apparatus from different oceanic regions, we prioritized the processes underlying AAP bacterial biogeographical patterns. The present analysis offers novel insights into the ecological distribution of marine AAP bacteria and highlights that physiological constraints play a key role in structuring AAP bacterial assemblages at a global scale. Salinity especially seems to favor lineage-specific adaptations. Moreover, by inferring the evolutionary history of habitat transitions, a substantial congruence between habitat and evolutionary relatedness was highlighted. The identification of ecological cohesive clades for AAP bacteria suggests that prediction of AAP bacterial assemblages is possible from marine habitat properties.

Aerobic Anoxygenic Photosynthesis Is Commonly Present within the Genus Limnohabitans

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-D5^T 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.

Predicting Species-Resolved Macronutrient Acquisition during Succession in a Model Phototrophic Biofilm Using an Integrated 'Omics Approach

The principles governing acquisition and interspecies exchange of nutrients in microbial communities and how those exchanges impact community productivity are poorly understood. Here, we examine energy and macronutrient acquisition in unicyanobacterial consortia for which species-resolved genome information exists for all members, allowing us to use multi-omic approaches to predict species' abilities to acquire resources and examine expression of resource-acquisition genes during succession. Metabolic reconstruction indicated that a majority of heterotrophic community members lacked the genes required to directly acquire the inorganic nutrients provided in culture medium, suggesting high metabolic interdependency. The sole primary producer in consortium UCC-O, cyanobacterium Phormidium sp. OSCR, displayed declining expression of energy harvest, carbon fixation, and nitrate and sulfate reduction proteins but sharply increasing phosphate transporter expression over 28 days. Most heterotrophic members likewise exhibited signs of phosphorus starvation during succession. Though similar in their responses to phosphorus limitation, heterotrophs displayed species-specific expression of nitrogen acquisition genes. These results suggest niche partitioning around nitrogen sources may structure the community when organisms directly compete for limited phosphate. Such niche complementarity around nitrogen sources may increase community diversity and productivity in phosphate-limited phototrophic communities.

Complete genome sequence of bacteriochlorophyll-synthesizing bacterium Porphyrobacter neustonensis DSM 9434

The genus Porphyrobacter belongs to aerobic anoxygenic phototrophic bacteria cluster. Porphyrobacter neustonensis DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll a as well as grow under aerobic conditions. It is the type species of the genus Porphyrobacter. Here we describe the characteristics of the strain DSM 9434, including the genome sequence and annotation, synthesis of BChl a, and metabolic pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain DSM 9434 encodes 46 genes which participate in BChl a synthesis and this investigation shed light on the evolution and functional implications regarding bacteriochlorophyll synthesis.

Aerobic anoxygenic phototrophs in gold mine tailings in Nopiming Provincial Park, Manitoba, Canada

A sampling trip to Central Gold Mine, Nopiming Provincial Park, Canada, was taken in September 2011. Abundance, distribution, and physiology of aerobic anoxygenic phototrophs (AAP) from 4 locations were studied. Enumeration revealed 14.6% of culturable microbes were AAP. Five strains (NM4.16, NM4.18, C4, C9, C11) were chosen for analysis. All grow best on complex media without vitamin requirements and with an optimal pH 7.0-8.0, with strain C4 preferring pH 6.0. Strain NM4.18 tolerates the highest pH 11.0. Optimal temperature for all is 28 °C (range of 2-37 °C except NM4.16, which survives 45 °C). Strains C9, C11, and NM4.18 grew in 1.0%, 2.0%, and 5.0% NaCl, respectively, while NM4.16 and C4 grew only without NaCl. Isolates were all highly resistant to toxic metal(oid) oxides: tellurite (1500 μg/mL, all), tellurate (1500 μg/mL, C11), selenite (5000 μg/mL, C9, C11, and NM4.18), selenate (1000 μg/mL, C9 and C11), and orthometavanadate and metavanadate (5000 μg/mL, C11 and NM4.18). They could reduce tellurite to the less toxic elemental tellurium. Full 16S rRNA gene sequencing revealed all strains are Alphaproteobacteria, with C4 and NM4.16 closely related to Porphyrobacter colymbi (99.4% and 99.7% sequence similarity, respectively), C9 to Brevundimonas variabilis (99.1%), C11 to Brevundimonas bacteroides (98.6%), and NM4.18 to Erythromonas ursincola (98.5%).

Towards long-read metagenomics: complete assembly of three novel genomes from bacteria dependent on a diazotrophic cyanobacterium in a freshwater lake co-culture

Here we report three complete bacterial genome assemblies from a PacBio shotgun metagenome of a co-culture from Upper Klamath Lake, OR. Genome annotations and culture conditions indicate these bacteria are dependent on carbon and nitrogen fixation from the cyanobacterium Aphanizomenon flos-aquae, whose genome was assembled to draft-quality. Due to their taxonomic novelty relative to previously sequenced bacteria, we have temporarily designated these bacteria as incertae sedis Hyphomonadaceae strain UKL13-1 (3,501,508 bp and 56.12% GC), incertae sedis Betaproteobacterium strain UKL13-2 (3,387,087 bp and 54.98% GC), and incertae sedis Bacteroidetes strain UKL13-3 (3,236,529 bp and 37.33% GC). Each genome consists of a single circular chromosome with no identified plasmids. When compared with binned Illumina assemblies of the same three genomes, there was ~7% discrepancy in total genome length. Gaps where Illumina assemblies broke were often due to repetitive elements. Within these missing sequences were essential genes and genes associated with a variety of functional categories. Annotated gene content reveals that both Proteobacteria are aerobic anoxygenic phototrophs, with Betaproteobacterium UKL13-2 potentially capable of phototrophic oxidation of sulfur compounds. Both proteobacterial genomes contain transporters suggesting they are scavenging fixed nitrogen from A. flos-aquae in the form of ammonium. Bacteroidetes UKL13-3 has few completely annotated biosynthetic pathways, and has a comparatively higher proportion of unannotated genes. The genomes were detected in only a few other freshwater metagenomes, suggesting that these bacteria are not ubiquitous in freshwater systems. Our results indicate that long-read sequencing is a viable method for sequencing dominant members from low-diversity microbial communities, and should be considered for environmental metagenomics when conditions meet these requirements.

Diversity of Phototrophic Genes Suggests Multiple Bacteria May Be Able to Exploit Sunlight in Exposed Soils from the Sør Rondane Mountains, East Antarctica

Microbial life in exposed terrestrial surface layers in continental Antarctica is faced with extreme environmental conditions, including scarcity of organic matter. Bacteria in these exposed settings can therefore be expected to use alternative energy sources such as solar energy, abundant during the austral summer. Using Illumina MiSeq sequencing, we assessed the diversity and abundance of four conserved protein encoding genes involved in different key steps of light-harvesting pathways dependent on (bacterio)chlorophyll (pufM, bchL/chlL, and bchX genes) and rhodopsins (actinorhodopsin genes), in exposed soils from the Sør Rondane Mountains, East Antarctica. Analysis of pufM genes, encoding a subunit of the type 2 photochemical reaction center found in anoxygenic phototrophic bacteria, revealed a broad diversity, dominated by Roseobacter- and Loktanella-like sequences. The bchL and chlL, involved in (bacterio)chlorophyll synthesis, on the other hand, showed a high relative abundance of either cyanobacterial or green algal trebouxiophyceael chlL reads, depending on the sample, while most bchX sequences belonged mostly to previously unidentified phylotypes. Rhodopsin-containing phototrophic bacteria could not be detected in the samples. Our results, while suggesting that Cyanobacteria and green algae are the main phototrophic groups, show that light-harvesting bacteria are nevertheless very diverse in microbial communities in Antarctic soils.

Abundance of Common Aerobic Anoxygenic Phototrophic Bacteria in a Coastal Aquaculture Area

Aerobic anoxygenic phototrophic bacteria (AAnPB) rely on not only heterotrophic but also phototrophic energy gain. AAnPB are known to have high abundance in oligotrophic waters and are the major portion of the bacterial carbon stock in the environment. In a yearlong study in an aquaculture area in the Uwa Sea, Japan, AAnPB, accounted for 4.7 to 24% of the total bacteria by count. Since the cell volume of AAnPB is 2.23 ± 0.674 times larger than the mean for total bacteria, AAnPB biomass is estimated to account for 10–53% of the total bacterial assemblage. By examining pufM gene sequence, a common phylogenetic AAnPB species was found in all sampling sites through the year. The common species and other season-specific species were phylogenetically close to unculturable clones recorded in the Sargasso Sea and Pacific Ocean. The present study suggests that the common species may be a cosmopolitan species with worldwide distribution that is abundant not only in the oligotrophic open ocean but also in eutrophic aquaculture areas.

Geographic Impact on Genomic Divergence as Revealed by Comparison of Nine Citromicrobial Genomes

Aerobic anoxygenic phototrophic bacteria (AAPB) are thought to be important players in oceanic carbon and energy cycling in the euphotic zone of the ocean. The genus Citromicrobium, widely found in oligotrophic oceans, is a member of marine alphaproteobacterial AAPB. Nine Citromicrobium strains isolated from the South China Sea, the Mediterranean Sea, or the tropical South Atlantic Ocean were found to harbor identical 16S rRNA sequences. The sequencing of their genomes revealed high synteny in major regions. Nine genetic islands (GIs) involved mainly in type IV secretion systems, flagellar biosynthesis, prophage, and integrative conjugative elements, were identified by a fine-scale comparative genomics analysis. These GIs played significant roles in genomic evolution and divergence. Interestingly, the coexistence of two different photosynthetic gene clusters (PGCs) was not only found in the analyzed genomes but also confirmed, for the first time, to our knowledge, in environmental samples. The prevalence of the coexistence of two different PGCs may suggest an adaptation mechanism for Citromicrobium members to survive in the oceans. Comparison of genomic characteristics (e.g., GIs, average nucleotide identity [ANI], single-nucleotide polymorphisms [SNPs], and phylogeny) revealed that strains within a marine region shared a similar evolutionary history that was distinct from that of strains isolated from other regions (South China Sea versus Mediterranean Sea). Geographic differences are partly responsible for driving the observed genomic divergences and allow microbes to evolve through local adaptation. Three Citromicrobium strains isolated from the Mediterranean Sea diverged millions of years ago from other strains and evolved into a novel group.

IMPORTANCE

Aerobic anoxygenic phototrophic bacteria are a widespread functional group in the upper ocean, and their abundance could be up to 15% of the total heterotrophic bacteria. To date, a great number of studies display AAPB biogeographic distribution patterns in the ocean; however, little is understood about the geographic isolation impact on the genome divergence of marine AAPB. In this study, we compare nine Citromicrobium genomes of strains that have identical 16S rRNA sequences but different ocean origins. Our results reveal that strains isolated from the same marine region share a similar evolutionary history that is distinct from that of strains isolated from other regions. These Citromicrobium strains diverged millions of years ago. In addition, the coexistence of two different PGCs is prevalent in the analyzed genomes and in environmental samples.

Phylogenetically Diverse Aerobic Anoxygenic Phototrophic Bacteria Isolated from Epilithic Biofilms in Tama River, Japan

The diversity of aerobic anoxygenic phototrophic (AAP) bacteria in freshwater environments, particularly in rivers, has not been examined in as much detail as in ocean environments. In the present study, we investigated the phylogenetic and physiological diversities of AAP bacteria in biofilms that developed on submerged stones in a freshwater river using culture methods. The biofilms collected were homogenized and inoculated on solid media and incubated aerobically in the dark. Sixty-eight red-, pink-, yellow-, orange-, or brown-colored colonies were isolated, and, of these, 28 isolates contained the photosynthetic pigment, bacteriochlorophyll (BChl) a. Phylogenetic analyses based on 16S rRNA gene sequences showed that the isolates were classified into 14 groups in 8 operational taxonomic units (OTUs) and distributed in the orders Rhodospirillales, Rhodobacterales, and Sphingomonadales of Alphaproteobacteria and in Betaproteobacteria. Physiological analyses confirmed that none of the representative isolates from any of the groups grew under anaerobic phototrophic conditions. Seven isolates in 4 OTUs showed a 16S rRNA gene sequence identity of 98.0% or less with any established species, suggesting the presence of previously undescribed species of AAP bacteria. Six isolates in 2 other OTUs had the closest relatives, which have not been reported to be AAP bacteria. Physiological comparisons among the isolates revealed differences in preferences for nutrient concentrations, BChl contents, and light-harvesting proteins. These results suggest that diverse and previously unknown AAP bacteria inhabit river biofilms.

Influence of selected environmental factors on the abundance of aerobic anoxygenic phototrophs in peat-bog lakes

Aerobic anoxygenic phototrophs (AAPs) are photoheterotrophic prokaryotes that are widespread in many limnic and marine environments. So far, little is known about their distribution in peat-bog lakes. Seventeen peat-bog lakes were sampled during three summer seasons 2009, 2011, and 2012, and the vertical distribution of AAPs was determined by infrared epifluorescence microscopy. The analysis demonstrated that in the surface layers of the studied lakes, AAP abundance ranged from 0.3 to 12.04 × 10(5) cells mL(-1), which represents <1 to 18.3 % of the total bacteria. The vertical distribution of AAPs confirmed their presence in the upper parts of the water column with minimum numbers in the anoxic bottom waters. We have shown that the AAP abundance was significantly positively correlated with the water pH, and the highest proportion of photoheterotrophs was found in peat-bog lakes with a pH between 6.7 and 7.6. Our results demonstrated an influence of water acidity on the abundance of AAPs, which may reflect a fundamental difference in the microbial composition between acidic and pH neutral peat-bog lakes.

A Comparison of 14 Erythrobacter Genomes Provides Insights into the Genomic Divergence and Scattered Distribution of Phototrophs

Aerobic anoxygenic phototrophic bacteria (AAPB) are bacteriochlorophyll a (Bchl a)-containing microbial functional population. Erythrobacter is the first genus that was identified to contain AAPB species. Here, we compared 14 Erythrobacter genomes: seven phototrophic strains and seven non- phototrophic strains. Interestingly, AAPB strains are scattered in this genus based on their phylogenetic relationships. All 14 strains could be clustered into three groups based on phylo-genomic analysis, average genomic nucleotide identity and the phylogeny of signature genes (16S rRNA and virB4 genes). The AAPB strains were distributed in three groups, and gain and loss of phototrophic genes co-occurred in the evolutionary history of the genus Erythrobacter. The organization and structure of photosynthesis gene clusters (PGCs) in seven AAPB genomes displayed high synteny of major regions except for few insertions. The 14 Erythrobacter genomes had a large range of genome sizes, from 2.72 to 3.60 M, and the sizes of the core and pan- genomes were 1231 and 8170 orthologous clusters, respectively. Integrative and conjugative elements (ICEs) were frequently identified in genomes we studied, which might play significant roles in shaping or contributing to the pan-genome of Erythrobacter. Our findings suggest the ongoing evolutionary divergence of Erythrobacter genomes and the scattered distribution characteristic of PGC.

The variability of light-harvesting complexes in aerobic anoxygenic phototrophs

Light-harvesting capacity was investigated in six species of aerobic anoxygenic phototrophic (AAP) bacteria using absorption spectroscopy, fluorescence emission spectroscopy, and pigment analyses. Aerobically grown AAP cells contained approx. 140-1800 photosynthetic reaction centers per cell, an order of magnitude less than purple non-sulfur bacteria grown semiaerobically. Three of the studied AAP species did not contain outer light-harvesting complexes, and the size of their reaction center core complexes (RC-LH1 core complexes) varied between 29 and 36 bacteriochlorophyll molecules. In AAP species containing accessory antennae, the size was frequently reduced, providing between 5 and 60 additional bacteriochlorophyll molecules. In Roseobacter litoralis, it was found that cells grown at a higher light intensity contained more reaction centers per cell, while the size of the light-harvesting complexes was reduced. The presented results document that AAP species have both the reduced number and size of light-harvesting complexes which is consistent with the auxiliary role of phototrophy in this bacterial group.

Picoplankton Bloom in Global South? A High Fraction of Aerobic Anoxygenic Phototrophic Bacteria in Metagenomes from a Coastal Bay (Arraial do Cabo--Brazil)

Marine habitats harbor a great diversity of microorganism from the three domains of life, only a small fraction of which can be cultivated. Metagenomic approaches are increasingly popular for addressing microbial diversity without culture, serving as sensitive and relatively unbiased methods for identifying and cataloging the diversity of nucleic acid sequences derived from organisms in environmental samples. Aerobic anoxygenic phototrophic bacteria (AAP) play important roles in carbon and energy cycling in aquatic systems. In oceans, those bacteria are widely distributed; however, their abundance and importance are still poorly understood. The aim of this study was to estimate abundance and diversity of AAPs in metagenomes from an upwelling affected coastal bay in Arraial do Cabo, Brazil, using in silico screening for the anoxygenic photosynthesis core genes. Metagenomes from the Global Ocean Sample Expedition (GOS) were screened for comparative purposes. AAPs were highly abundant in the free-living bacterial fraction from Arraial do Cabo: 23.88% of total bacterial cells, compared with 15% in the GOS dataset. Of the ten most AAP abundant samples from GOS, eight were collected close to the Equator where solar irradiation is high year-round. We were able to assign most retrieved sequences to phylo-groups, with a particularly high abundance of Roseobacter in Arraial do Cabo samples. The high abundance of AAP in this tropical bay may be related to the upwelling phenomenon and subsequent picoplankton bloom. These results suggest a link between upwelling and light abundance and demonstrate AAP even in oligotrophic tropical and subtropical environments. Longitudinal studies in the Arraial do Cabo region are warranted to understand the dynamics of AAP at different locations and seasons, and the ecological role of these unique bacteria for biogeochemical and energy cycling in the ocean.

Single-cell activity of freshwater aerobic anoxygenic phototrophic bacteria and their contribution to biomass production

Aerobic anoxygenic phototrophic (AAP) bacteria are photoheterotrophs that despite their low abundances have been hypothesized to play an ecologically and biogeochemically important role in aquatic systems. Characterizing this role requires a better understanding of the in situ dynamics and activity of AAP bacteria. Here we provide the first assessment of the single-cell activity of freshwater AAP bacteria and their contribution to total bacterial production across lakes spanning a wide trophic gradient, and explore the role of light in regulating AAP activity. The proportion of cells that were active in leucine incorporation and the level of activity per cell were consistently higher for AAP than for bulk bacteria across lakes. As a result, AAP bacteria contributed disproportionately more to total bacterial production than to total bacterial abundance. Interestingly, although environmentally driven patterns in activity did not seem to differ largely between AAP and bulk bacteria, their response to light did, and exposure to light resulted in increases in the proportion of active AAP bacteria with no clear effect on their cell-specific activity. This suggests that light may play a role in the activation of AAP bacteria, enabling these photoheterotrophs to contribute more to the carbon cycle than suggested by their abundance.

The Draft Genome Sequence of Sphingomonas sp. Strain FukuSWIS1, Obtained from Acidic Lake Grosse Fuchskuhle, Indicates Photoheterotrophy and a Potential for Humic Matter Degradation

Sphingomonas spp. are Alphaproteobacteria considered to be versatile bacteria that can utilize a variety of natural substrates available in terrestrial and aquatic systems. Sphingomonas sp. strain FukuSWIS1 was isolated from the eutrophic and acidic freshwater Lake Grosse Fuchskuhle in northeastern Germany. The strain has a genome size of 3.89 Mb, possesses a set of photosynthetic genes, and expresses photopigment BChl a under oxic conditions. Thus, this strain belongs to the aerobic anoxygenic phototrophic (AAP) bacteria, which are most likely involved in humic matter degradation as indicated by the presence of organic compound mineralizing genes.

Extremely 'vanadiphilic' multiply metal-resistant and halophilic aerobic anoxygenic phototrophs, strains EG13 and EG8, from hypersaline springs in Canada

Two pinkish peach-colored strains of obligately aerobic phototrophic bacteria, EG13 and EG8, were isolated from a saline spring effluent stream in west central Manitoba, Canada. The strains possessed bacteriochlorophyll a incorporated into a typical purple bacterial light-harvesting complex 1 (870 nm) and reaction center (801 nm). Analysis of 16S rRNA gene sequences indicated 100% identity among the isolates and 99% similarity to Roseovarius tolerans EL-172(T). The strains were physiologically well adapted to high salinity (0-22%), fluctuating pH (7-12) and temperature (7-40 °C) of the exposed hypersaline stream of East German Creek. EG8 and EG13 were also highly resistant to the toxic metal(loid) oxyanions tellurite, selenite and metavanadate (≥1000 μg/ml each). Most intriguingly, growth and pigment production of EG13 on glutamate minimal medium was stimulated by 1000-10000 μg/ml of sodium metavanadate compared to metal-free conditions. Phylogenetic analysis and phenotypic properties such as pigment composition and morphology indicate close relatedness to Roseovarius genus.

Exchange and complementation of genes coding for photosynthetic reaction center core subunits among purple bacteria

A mutant of the phototrophic species belonging to the β-proteobacteria, Rubrivivax gelatinosus, lacking the photosynthetic growth ability was constructed by the removal of genes coding for the L, M, and cytochrome subunits of the photosynthetic reaction center complex. The L, M, and cytochrome genes derived from five other species of proteobacteria, Acidiphilium rubrum, Allochromatium vinosum, Blastochloris viridis, Pheospirillum molischianum, and Roseateles depolymerans, and the L and M subunits from two other species, Rhodobacter sphaeroides and Rhodopseudomonas palustris, respectively, have been introduced into this mutant. Introduction of the genes from three of these seven species, Rte. depolymerans, Ach. vinosum, and Psp. molischianum, restored the photosynthetic growth ability of the mutant of Rvi. gelatinosus, although the growth rates were 1.5, 9.4, and 10.7 times slower, respectively, than that of the parent strain. Flash-induced kinetic measurements for the intact cells of these three mutants showed that the photo-oxidized cytochrome c bound to the introduced reaction center complex could be rereduced by electron donor proteins of Rvi. gelatinosus with a t1/2 of less than 10 ms. The reaction center core subunits of photosynthetic proteobacteria appear to be exchangeable if the sequence identities of the LM core subunits between donor and acceptor species are high enough, i.e., 70% or more.

Environmental controls and composition of anoxygenic photoheterotrophs in ultraoligotrophic high-altitude lakes (Central Pyrenees)

The phylogenetic composition of freshwater anoxygenic photoheterotrophs (APs) has been poorly investigated as compared with their marine counterparts. In this study, we explored a set of ultraoligotrophic cold high mountain lakes (Central Pyrenees, Spain) by both pufM gene denaturing gradient gel electrophoresis fingerprinting, and cloning and sequencing of selected lakes samples. Different ranges of limnological and physico-chemical values were explored as environmental drivers of APs richness and composition. We did not observe significant relationships between richness/diversity of pufM and any of the limnological characteristics measured or trophic status, but a negative correlation with ammonia concentration. Conductivity, pH and nitrate concentration were significantly related to changes in APs community composition, whereas lake area, altitude, temperature and trophic status did not. Most of the sequences (> 85%) had the pufM sequences of Limnohabitans (Betaproteobacteria) as the closest relative in databases, whereas less abundant clones were more closely related to Rhodobacter, Sulfitobacter and Brevundimonas (Alphaproteobacteria), in agreement with 16S rRNA gene sequences previously found in the area. Congregibacter-like Gammaproteobacteria were not detected. Comparison with available studies in inland waters showed taxonomic partitioning along salinity gradients, and Congregibacter-like sequences restricted to high saline conditions in continental water bodies.

Temporal changes and altitudinal distribution of aerobic anoxygenic phototrophs in mountain lakes

Aerobic anoxygenic phototrophs (AAPs) are bacteriochlorophyll a-containing microorganisms that use organic substrates for growth but can supplement their energy requirements with light. They have been reported from various marine and limnic environments; however, their ecology remains largely unknown. Here infrared epifluorescence microscopy was used to monitor temporal changes in AAPs in the alpine lake Gossenköllesee, located in the Tyrolean Alps, Austria. AAP abundance was low (10(3) cells ml(-1)) until mid-July and reached a maximum of ∼1.3 × 10(5) cells ml(-1) (29% of all prokaryotes) in mid-September. We compared the studied lake with other mountain lakes located across an altitudinal gradient (913 to 2,799 m above sea level). The concentration of dissolved organic carbon and water transparency seem to be the main factors influencing AAP abundance during the seasonal cycle as well as across the altitudinal gradient. While the AAP populations inhabiting the alpine lakes were composed of intensely pigmented large rods (5 to 12 μm), the lakes below the tree line were inhabited by a variety of smaller morphotypes. Analysis of pufM diversity revealed that AAPs in Gossenköllesee were almost exclusively Sphingomonadales species, which indicates that AAP communities inhabiting alpine lakes are relatively homogeneous compared to those in low-altitude lakes.

Extending the limits of natural photosynthesis and implications for technical light harvesting

Photosynthetic organisms provide, directly or indirectly, the energy that sustains life on earth by harvesting light from the sun. The amount of light impinging on the surface of the earth vastly surpasses the energy needs of life including man. Harvesting the sun is, therefore, an option for a sustainable energy source: directly by improving biomass production, indirectly by coupling it to the production of hydrogen for fuel or, conceptually, by using photosynthetic strategies for technological solutions based on non-biological or hybrid materials. In this review, we summarize the various light climates on earth, the primary reactions responsible for light harvesting and transduction to chemical energy in photosynthesis, and the mechanisms of competitively adapting the photosynthetic apparatus to the ever-changing light conditions. The focus is on oxygenic photosynthesis, its adaptation to the various light-climates by specialized pigments and on the extension of its limits by the evolution of red-shifted chlorophylls. The implications for potential technical solutions are briefly discussed.