Contribution of aerobic photoheterotrophic bacteria to the carbon cycle in the ocean

Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network

BACKGROUND

Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of the microbial food chain. Despite their considerable contribution to the transformation of organic matter in marine environments, relatively little is still known about their community structure and ecology at fine-scale taxonomic resolution. Up to date, there is no comprehensive (i.e. qualitative and quantitative) analysis of their community composition in the Adriatic Sea.

RESULTS

Analysis was based on pufM gene metabarcoding and quantitative FISH-IR approach with the use of artificial neural network. Significant seasonality was observed with regards to absolute abundances (maximum average abundances in spring 2.136 ± 0.081 × 104 cells mL-1, minimum in summer 0.86 × 104 cells mL-1), FISH-IR groups (Roseobacter clade prevalent in autumn, other Alpha- and Gammaproteobacteria in summer) and pufM sequencing data agglomerated at genus-level. FISH-IR results revealed heterogeneity with the highest average relative contribution of AAPs assigned to Roseobacter clade (37.66%), followed by Gammaproteobacteria (35.25%) and general Alphaproteobacteria (31.15%). Community composition obtained via pufM sequencing was dominated by Gammaproteobacteria clade NOR5/OM60, specifically genus Luminiphilus, with numerous rare genera present in relative abundances below 1%. The use of artificial neural network connected this community to biotic (heterotrophic bacteria, HNA and LNA bacteria, Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic nanoflagellates, bacterial production) and abiotic environmental factors (temperature, salinity, chlorophyll a and nitrate, nitrite, ammonia, total nitrogen, silicate, and orthophosphate concentration). A type of neural network, neural gas analysis at order-, genus- and ASV-level, resulted in five distinct best matching units (representing particular environments) and revealed that high diversity was generally independent of temperature, salinity, and trophic status of the environment, indicating a potentially dissimilar behaviour of aerobic anoxygenic phototrophs compared to the general bacterioplankton.

CONCLUSION

This research represents the first comprehensive analysis of aerobic anoxygenic phototrophs in the Adriatic Sea on a trophic gradient during a year-round period. This study is also one of the first reports of their genus-level ecology linked to biotic and abiotic environmental factors revealed by unsupervised neural network algorithm, paving the way for further research of substantial contribution of this important bacterial functional group to marine ecosystems.

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).

Growth and mortality of aerobic anoxygenic phototrophs in the North Pacific Subtropical Gyre

Aerobic anoxygenic phototrophic (AAP) bacteria harvest light energy using bacteriochlorophyll-containing reaction centers to supplement their mostly heterotrophic metabolism. While their abundance and growth have been intensively studied in coastal environments, much less is known about their activity in oligotrophic open ocean regions. Therefore, we combined in situ sampling in the North Pacific Subtropical Gyre, north of O'ahu island, Hawaii, with two manipulation experiments. Infra-red epifluorescence microscopy documented that AAP bacteria represented approximately 2% of total bacteria in the euphotic zone with the maximum abundance in the upper 50 m. They conducted active photosynthetic electron transport with maximum rates up to 50 electrons per reaction center per second. The in situ decline of bacteriochlorophyll concentration over the daylight period, an estimate of loss rates due to predation, indicated that the AAP bacteria in the upper 50 m of the water column turned over at rates of 0.75-0.90 d-1. This corresponded well with the specific growth rate determined in dilution experiments where AAP bacteria grew at a rate 1.05 ± 0.09 d-1. An amendment of inorganic nitrogen to obtain N:P = 32 resulted in a more than 10 times increase in AAP abundance over 6 days. The presented data document that AAP bacteria are an active part of the bacterioplankton community in the oligotrophic North Pacific Subtropical Gyre and that their growth was mostly controlled by nitrogen availability and grazing pressure.IMPORTANCEMarine bacteria represent a complex assembly of species with different physiology, metabolism, and substrate preferences. We focus on a specific functional group of marine bacteria called aerobic anoxygenic phototrophs. These photoheterotrophic organisms require organic carbon substrates for growth, but they can also supplement their metabolic needs with light energy captured by bacteriochlorophyll. These bacteria have been intensively studied in coastal regions, but rather less is known about their distribution, growth, and mortality in the oligotrophic open ocean. Therefore, we conducted a suite of measurements in the North Pacific Subtropical Gyre to determine the distribution of these organisms in the water column and their growth and mortality rates. A nutrient amendment experiment showed that aerobic anoxygenic phototrophs were limited by inorganic nitrogen. Despite this, they grew more rapidly than average heterotrophic bacteria, but their growth was balanced by intense grazing pressure.

Metagenomic insight into the acidophilic functional communities driving elemental geochemical cycles in an acid mine drainage lake

Acidophiles play a key role in the generation, evolution and attenuation of acid mine drainage (AMD), which is characterized by strong acidity (pH<3.5) and high metal concentrations. In this study, the seasonal changes of acidophilic communities and their roles in elemental cycling in an AMD lake (pH∼3.0) in China were analyzed through metagenomics. The results showed eukaryotic algae thrived in the lake, and Coccomyxa was dominant in January (38.1%) and May (33.9%), while Chlorella in July (9.5%). The extensive growth of Chlamydomonas in December (22.7%) resulted in an ultrahigh chlorophyll a concentration (587 μg/L), providing abundant organic carbon for the ecosystem. In addition, the iron-oxidizing and nitrogen-fixing bacterium Ferrovum contributed to carbon fixation. Ammonia oxidation likely occurred in the acidic lake, as was revealed by archaea Ca. Nitrosotalea. To gain a competitive advantage in the nutrient-poor environment, some acidophiles exhibited facultative characteristics, e.g. the most abundant bacterium Acidiphilium utilized both organic and inorganic carbon, and obtained energy from organic matter, inorganic sulfur, and sunlight simultaneously. It was suggested that sunlight, rather than chemical energy of reduced iron-sulfur was the major driver of elemental cycling in the AMD lake. The results are beneficial to the development of bioremediation strategies for AMD.

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.

Paddy cultivation in degraded karst wetland soil can significantly improve the physiological and ecological functions of carbon-fixing resident microorganisms

Microorganisms play an important role in carbon fixation in karst wetland soils. However, the carbon fixation capacity of karst wetland soils and active microorganisms involved in the carbon fixation process are poorly understood. In this study, carbon fixation capacity and active microorganisms involved in the fixation of inorganic carbon into organic carbon were studied in native, naturally degraded, and reclaimed karst wetland soils by the combination of stable isotope probing (SIP) and high-throughput sequencing. Under light conditions, the soil carbon fixation capacity ranked: the reclaimed wetland soil (1.58 mg C kg-1 day-1) > native wetland soil (1.43 mg C kg-1 day-1) > degraded wetland soil (0.62 mg C kg-1 day-1). In the dark, the soils ranked: the native wetland soil (0.24 mg C kg-1 day-1) > reclaimed wetland soil (0.18 mg C kg-1 day-1) > degraded wetland soil (0.06 mg C kg-1 day-1). Active microorganisms fixing inorganic carbon in the karst wetland soils were mainly Sulfurovum, Thermovirga, Dethiosulfatibacter, Allochromatium, Methylorubrum, and Bradyrhizobium. Thus, paddy cultivation can restore the carbon fixation capacity of microorganisms in the degraded karst wetland soil. This study provides an experimental basis for improving soil carbon fixation capacity and repairing degraded soil in karst wetlands.

Engineering artificial photosynthesis based on rhodopsin for CO2 fixation

Microbial rhodopsin, a significant contributor to sustaining life through light harvesting, holds untapped potential for carbon fixation. Here, we construct an artificial photosynthesis system which combines the proton-pumping ability of rhodopsin with an extracellular electron uptake mechanism, establishing a pathway to drive photoelectrosynthetic CO2 fixation by Ralstonia eutropha (also known as Cupriavidus necator) H16, a facultatively chemolithoautotrophic soil bacterium. R. eutropha is engineered to heterologously express an extracellular electron transfer pathway of Shewanella oneidensis MR-1 and Gloeobacter rhodopsin (GR). Employing GR and the outer-membrane conduit MtrCAB from S. oneidensis, extracellular electrons and GR-driven proton motive force are integrated into R. eutropha's native electron transport chain (ETC). Inspired by natural photosynthesis, the photoelectrochemical system splits water to supply electrons to R. eutropha via the Mtr outer-membrane route. The light-activated proton pump - GR, supported by canthaxanthin as an antenna, powers ATP synthesis and reverses the ETC to regenerate NADH/NADPH, facilitating R. eutropha's biomass synthesis from CO2. Overexpression of a carbonic anhydrase further enhances CO2 fixation. This artificial photosynthesis system has the potential to advance the development of efficient photosynthesis, redefining our understanding of the ecological role of microbial rhodopsins in nature.

DOM Associates with Greenhouse Gas Emissions in Chinese Rivers under Diverse Land Uses

Growing evidence indicates that rivers are hotspots of greenhouse gas (GHG) emissions and play multiple roles in the global carbon budget. However, the roles of terrestrial carbon from land use in river GHG emissions remain largely unknown. We studied the microbial composition, dissolved organic matter (DOM) properties, and GHG emission responses to different landcovers in rivers (n = 100). The bacterial community was mainly constrained by land-use intensity, whereas the fungal community was mainly controlled by DOM chemical composition (e.g., terrestrial DOM with high photoreactivity). Anthropogenic stressors (e.g., land-use intensity, gross regional domestic product, and total population) were the main factors affecting chromophoric DOM (CDOM). DOM biodegradability exhibited a positive correlation with CDOM and contributed to microbial activity for DOM transformation. Variations in CO2 and CH4 emissions were governed by the biodegradation or photomineralization of dissolved organic carbon derived from autotrophic DOM and were indirectly affected by land use via changes in DOM properties and water chemistry. Because the GHG emissions of rivers offset some of the climatic benefits of terrestrial carbon (or ocean) sinks, intensified urban land use inevitably alters carbon cycling and changes the regional microclimate.

Cellular Damage of Bacteria Attached to Senescent Phytoplankton Cells as a Result of the Transfer of Photochemically Produced Singlet Oxygen: A Review

Several studies set out to explain the presence of high proportions of photooxidation products of cis-vaccenic acid (generally considered to be of bacterial origin) in marine environments. These studies show that these oxidation products result from the transfer of singlet oxygen from senescent phytoplankton cells to the bacteria attached to them in response to irradiation by sunlight. This paper summarizes and reviews the key findings of these studies, i.e., the demonstration of the process at work and the effect of different parameters (intensity of solar irradiance, presence of bacterial carotenoids, and presence of polar matrices such as silica, carbonate, and exopolymeric substances around phytoplankton cells) on this transfer. A large part of this review looks at how this type of alteration of bacteria can affect the preservation of algal material in the marine environment, especially in polar regions where conditions drive increased transfer of singlet oxygen from sympagic algae to bacteria.

Characterisation of the photosynthetic complexes from the marine gammaproteobacterium Congregibacter litoralis KT71

Possibly the most abundant group of anoxygenic phototrophs are marine photoheterotrophic Gammaproteobacteria belonging to the NOR5/OM60 clade. As little is known about their photosynthetic apparatus, the photosynthetic complexes from the marine phototrophic bacterium Congregibacter litoralis KT71 were purified and spectroscopically characterised. The intra-cytoplasmic membranes contain a smaller amount of photosynthetic complexes when compared with anaerobic purple bacteria. Moreover, the intra-cytoplasmic membranes contain only a minimum amount of peripheral LH2 complexes. The complexes are populated by bacteriochlorophyll a, spirilloxanthin and two novel ketocarotenoids, with biophysical and biochemical properties similar to previously characterised complexes from purple bacteria. The organization of the RC-LH1 complex has been further characterised using cryo-electron microscopy. The overall organisation is similar to the complex from the gammaproteobacterium Thermochromatium tepidum, with the type-II reaction centre surrounded by a slightly elliptical LH1 antenna ring composed of 16 αβ-subunits with no discernible gap or pore. The RC-LH1 and LH2 apoproteins are phylogenetically related to other halophilic species but LH2 also to some alphaproteobacterial species. It seems that the reduction of light-harvesting apparatus and acquisition of novel ketocarotenoids in Congregibacter litoralis KT71 represent specific adaptations for operating the anoxygenic photosynthesis under aerobic conditions at sea.

Spatial and temporal dynamics at an actively silicifying hydrothermal system

Steep Cone Geyser is a unique geothermal feature in Yellowstone National Park (YNP), Wyoming, actively gushing silicon-rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone's outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM, respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation <32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophile Thermocrinis dominates the hydrothermal source biofilm community, and the thermophiles Meiothermus and Leptococcus dominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such as Leptococcus, Chloroflexus, and Chloracidobacterium act as primary producers for the system, supporting heterotrophic growth of taxa such as Raineya, Tepidimonas, and Meiothermus. Community dynamics illustrate large changes yearly driven by abundance shifts of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.

Transcriptome and Deletion Mutant Analyses Revealed that an RpoH Family Sigma Factor Is Essential for Photosystem Production in Roseateles depolymerans under Carbon Starvation

Roseateles depolymerans is an obligately aerobic bacterium that produces a photosynthetic apparatus only under the scarcity of carbon substrates. We herein examined changes in the transcriptomes of R. depolymerans cells to clarify the expression of photosynthesis genes and their upstream regulatory factors under carbon starvation. Transcriptomes 0, 1, and 6‍ ‍h after the depletion of a carbon substrate indicated that transcripts showing the greatest variations (a 500-fold increase [6 h/0 h]) were light-harvesting proteins (PufA and PufB). Moreover, loci with more than 50-fold increases (6 h/0‍ ‍h) were fully related to the photosynthetic gene cluster. Among 13 sigma factor genes, the transcripts of a sigma 70 family sigma factor related to RpoH (SP70) increased along photosynthesis genes under starvation; therefore, a knockout experiment of SP70 was performed. ΔSP70 mutants were found to lack photosynthetic pigments (carotenoids and bacteriochlo-rophyll a) regardless of carbon starvation. We also examined the effects of heat stress on ΔSP70 mutants, and found that SP70 was also related to heat stress tolerance, similar to other RpoH sigma factors (while heat stress did not trigger photosystem production). The deficient accumulation of photosynthetic pigments and the heat stress tolerance of ΔSP70 mutants were both complemented by the introduction of an intact SP70 gene. Furthermore, the transcription of photosynthetic gene operons (puf, puh, and bch) was markedly reduced in the ΔSP70 mutant. The RpoH homologue SP70 was concluded to be a sigma factor that is essential for the transcription of photosynthetic gene operons in R. depolymerans.

The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus

Erythrobacter is an important and widespread bacterial genus in the ocean. However, our knowledge about their phages is still rare. Here, a novel lytic phage vB_EliS-L02, infecting Erythrobacter litoralis DSM 8509, was isolated and purified from Sanggou Bay seawater, China. Morphological observation revealed that the phage belonged to Cbk-like siphovirus, with a long prolate head and a long tail. The host range test showed that phage vB_EliS-L02 could only infect a few strains of Erythrobacter, demonstrating its potential narrow-host range. The genome size of vB_EliS-L02 was 150,063 bp with a G+C content of 59.43%, encoding 231 putative open reading frames (ORFs), but only 47 were predicted to be functional domains. Fourteen auxiliary metabolic genes were identified, including phoH that may confer vB_EliS-L02 the advantage of regulating phosphate uptake and metabolism under a phosphate-limiting condition. Genomic and phylogenetic analyses indicated that vB_EliS-L02 was most closely related to the genus Lacusarxvirus with low similarity (shared genes < 30%, and average nucleotide sequence identity < 70%), distantly from other reported phages, and could be grouped into a novel viral genus cluster, in this study as Eliscbkvirus. Meanwhile, the genus Eliscbkvirus and Lacusarxvirus stand out from other siphoviral genera and could represent a novel subfamily within Siphoviridae, named Dolichocephalovirinae-II. Being a representative of an understudied viral group with manifold adaptations to the host, phage vB_EliS-L02 could improve our understanding of the virus–host interactions and provide reference information for viral metagenomic analysis in the ocean.

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.

Photoheterotrophy by aerobic anoxygenic bacteria modulates carbon fluxes in a freshwater lake

Lakes are a significant component of the global carbon cycle. Respiration exceeds net primary production in most freshwater lakes, making them a source of CO₂ to the atmosphere. Driven by heterotrophic microorganisms, respiration is assumed to be unaffected by light, thus it is measured in the dark. However, photoheterotrophs, such as aerobic anoxygenic photoheterotrophic (AAP) bacteria that produce ATP via photochemical reactions, substantially reduce respiration in the light. They are an abundant and active component of bacterioplankton, but their photoheterotrophic contribution to microbial community metabolism remains unquantified. We showed that the community respiration rate in a freshwater lake was reduced by 15.2% (95% confidence interval (CI): 6.6-23.8%) in infrared light that is usable by AAP bacteria but not by primary producers. Moreover, significantly higher assimilation rates of glucose (18.1%; 7.8-28.4%), pyruvate (9.5%; 4.2-14.8%), and leucine (5.9%; 0.1-11.6%) were measured in infrared light. At the ecosystem scale, the amount of CO₂ from respiration unbalanced by net primary production was by 3.69 × 10⁹ g CO₂ lower over these two sampling seasons when measured in the infrared light. Our results demonstrate that dark measurements of microbial activity significantly bias the carbon fluxes, providing a new paradigm for their quantification in aquatic environments.

Insights into carbon-fixation pathways through metagonomics in the sediments of deep-sea cold seeps

Carbon fixation by chemoautotrophic microorganisms in the dark ocean has a major impact on global carbon cycling and ecological relationships in the ocean's interior. At present, six pathways of autotrophic carbon fixation have been found: the Calvin cycle, the reductive Acetyl-CoA or Wood-Ljungdahl pathway (rAcCoA), the reductive tricarboxylic acid cycle (rTCA), the 3-hydroxypropionate bicycle (3HP), the 3-hydroxypropionate/4-hydroxybutyrate cycle (3HP/4HB), and the dicarboxylate/4-hydroxybutyrate cycle (DC/4HB). Although our knowledge about carbon fixation pathways in the ocean has increased significantly, carbon fixation pathways in the cold seeps are still unknown. In this study, we collected sediment samples from two cold seeps and one trough in the south China sea (SCS), and investigated with metagenomic and metagenome assembled genomes (MAGs). We found that six autotrophic carbon fixation pathways present in the cold seeps and trough with rTCA cycle was the most common pathway, whose genes were particularly high in the cold seeps and increased with sediment depths; the rAcCoA cycle mainly occurred in the cold seep regions, and the abundance of module genes increased with sediment depths. We also elucidated members of chemoautotrophic microorganisms involved in these six carbon-fixation pathways. The rAcCoA, rTCA and DC/4-HB cycles required significantly less energy probably play an important role in the deep-sea environments, especially in the cold seeps. This study provided metabolic insights into the carbon fixation pathways in the cold seeps, and laid the foundation for future detailed study on processes and rates of carbon fixation in the deep-sea ecosystems.

Phylogenetic diversity and spatiotemporal dynamics of bacterial and microeukaryotic plankton communities in Gwangyang Bay of the Korean Peninsula

Nutrient dynamics function globally, flowing from rivers to the ocean (estuarine–coastal zone), and are vulnerable to climate change. Microbial habitats can be affected by marine nutrient dynamics and may provide a clue to predict microbial responses to environmental heterogeneity in estuarine–coastal zones. We surveyed surface seawater in Gwangyang Bay, a semi-enclosed estuary in Korea, from 2016 to 2018 using a metabarcoding approach with prokaryotic 16S and eukaryotic 18S rRNA genes. Bacterial and microeukaryotic communities in these waters showed distinct local communities in response to environmental heterogeneity and community transition at spatiotemporal scales in the estuarine–coastal zone. The relative abundance of prokaryotic and eukaryotic operational taxonomic units suggested a microbial trophic interaction in the Gwangyang Bay waters. We found that the community assembly process in prokaryotic communities was primarily influenced by biological interaction (immigration–emigration), whereas that in eukaryotic communities was more affected by environmental stress (habitat specificity) rather than by biotic factors. Our findings in the Gwangyang Bay waters may provide information on underlying (biotic or abiotic) factors of the assembly process in microbial communities in the estuarine–coastal zone.

Seasonal fluctuations in symbiotic bacteria and their role in environmental adaptation of the scleractinian coral Acropora pruinosa in high-latitude coral reef area of the South China Sea

Coral-associated bacterial communities are paramount for coral ecosystems and holobiont health. However, the role of symbiotic bacteria in the adaptation of high-latitude corals to seasonal fluctuations remains underexplored. Therefore, we used 16S rRNA-based high-throughput sequencing to analyze the symbiotic bacterial diversity, composition, and core bacterial community in high-latitude coral and explored the seasonal fluctuation characteristics of symbiotic bacterial communities. We found that bacterial richness and α-diversity changed significantly across different seasons. Additionally, the community structure recombined seasonally, with different dominant bacterial phyla and genera in different seasons. However, the symbiotic bacterial community structures of Acropora pruinosa in winter and spring were similar. Proteobacteria were the dominant bacteria in spring, autumn, and winter. In summer, the dominant bacterial taxa were Bacteroidota and Proteobacteria. Ralstonia was the dominant bacterial genus in spring and winter, whereas in autumn, BD1-7_clade was dominant. Linear discriminant analysis effect size identified 20 abundant genera between the different groups. Core microbiome analysis revealed that 12 core bacterial operational taxonomic units were associated with A. pruinosa in all seasons, seven of which varied with the seasons, changing between dominant and rare. Distance-based redundancy and variation partitioning analyses revealed that sea surface temperature was the major contributor of variation in the microbial community structure. We hypothesized that the high diversity and abundance of symbiotic bacteria and the increase in Prosthecochloris abundance in coral in summer can help A. pruinosa maintain its physiological functions, ameliorating the negative physiological effects of the decrease in Symbiodiniaceae density under high-temperature stress. Thus, the rapid reorganization of the symbiotic bacterial community structure and core microflora in different seasons may allow the corals to adapt to large seasonal environmental fluctuations. In conclusion, seasonal variation of bacteria plays an important role in coral adaptation to large environmental fluctuations.

Proteorhodopsin Phototrophy in Antarctic Coastal Waters

Microbial proton-pumping rhodopsins are considered the simplest strategy among phototrophs to conserve energy from light. Proteorhodopsins are the most studied rhodopsins thus far because of their ubiquitous presence in the ocean, except in Antarctica, where they remain understudied. We analyzed proteorhodopsin abundance and transcriptional activity in the Western Antarctic coastal seawaters. Combining quantitative PCR (qPCR) and metagenomics, the relative abundance of proteorhodopsin-bearing bacteria accounted on average for 17, 3.5, and 29.7% of the bacterial community in Chile Bay (South Shetland Islands) during 2014, 2016, and 2017 summer-autumn, respectively. The abundance of proteorhodopsin-bearing bacteria changed in relation to environmental conditions such as chlorophyll a and temperature. Alphaproteobacteria, Gammaproteobacteria, and Flavobacteriia were the main bacteria that transcribed the proteorhodopsin gene during day and night. Although green light-absorbing proteorhodopsin genes were more abundant than blue-absorbing ones, the latter were transcribed more intensely, resulting in >50% of the proteorhodopsin transcripts during the day and night. Flavobacteriia were the most abundant proteorhodopsin-bearing bacteria in the metagenomes; however, Alphaproteobacteria and Gammaproteobacteria were more represented in the metatranscriptomes, with qPCR quantification suggesting the dominance of the active SAR11 clade. Our results show that proteorhodopsin-bearing bacteria are prevalent in Antarctic coastal waters in late austral summer and early autumn, and their ecological relevance needs to be elucidated to better understand how sunlight energy is used in this marine ecosystem. IMPORTANCE Proteorhodopsin-bearing microorganisms in the Southern Ocean have been overlooked since their discovery in 2000. The present study identify taxonomy and quantify the relative abundance of proteorhodopsin-bearing bacteria and proteorhodopsin gene transcription in the West Antarctic Peninsula's coastal waters. This information is crucial to understand better how sunlight enters this marine environment through alternative ways unrelated to chlorophyll-based strategies. The relative abundance of proteorhodopsin-bearing bacteria seems to be related to environmental parameters (e.g., chlorophyll a, temperature) that change yearly at the coastal water of the West Antarctic Peninsula during the austral late summers and early autumns. Proteorhodopsin-bearing bacteria from Antarctic coastal waters are potentially able to exploit both the green and blue spectrum of sunlight and are a prevalent group during the summer in this polar environment.

Harnessing Solar Energy using Phototrophic Microorganisms: A Sustainable Pathway to Bioenergy, Biomaterials, and Environmental Solutions

Phototrophic microorganisms (microbial phototrophs) use light as an energy source to carry out various metabolic processes producing biomaterials and bioenergy and supporting their own growth. Among them, microalgae and cyanobacteria have been utilized extensively for bioenergy, biomaterials, and environmental applications. Their superior photosynthetic efficiency, lipid content, and shorter cultivation time compared to terrestrial biomass make them more suitable for efficient production of bioenergy and biomaterials. Other phototrophic microorganisms, especially anoxygenic phototrophs, demonstrated the ability to survive and flourish while producing renewable energy and high-value products under harsh environmental conditions. This review presents a comprehensive overview of microbial phototrophs on their (i) production of bioenergy and biomaterials, (ii) emerging and innovative applications for environmental conservation, mitigation, and remediation, and (iii) physical, genetic, and metabolic pathways to improve light harvesting and biomass/biofuel/biomaterial production. Both physical (e.g., incremental irradiation) and genetic approaches (e.g., truncated antenna) are implemented to increase the light-harvesting efficiency. Increases in biomass yield and metabolic products are possible through the manipulation of metabolic pathways and selection of a proper strain under optimal cultivation conditions and downstream processing, including harvesting, extraction, and purification. Finally, the current barriers in harnessing solar energy using phototrophic microorganisms are presented, and future research perspectives are discussed, such as integrating phototrophic microorganisms with emerging technologies.

Spatial and temporal distribution of aerobic anoxygenic phototrophic bacteria: key functional groups in biological soil crusts

Several significant ecosystem services are performed by biological soil crusts (BSCs) in drylands, wherein photoautotrophic microorganisms are commonly critical contributors. However, aerobic anoxygenic phototrophic bacteria (AAnPB) are rarely reported in BSCs, despite being the second major branch of Earth's phototrophic microbes. Here, we collected different types of BSCs and their subsoils from temperate deserts, investigated distributions of AAnPB communities among BSCs using cultivation and high-throughput sequencing approaches, predicted keystone species by co-occurrence network analysis, and verified their effects on BSCs formation through microcosm experiments. The absolute abundances and diversity of AAnPB were higher in BSCs and were closely related with BSCs successional stages, as well as soil organic carbon contents. AAnPB communities in both BSCs and their subsoils were dominated by Proteobacteria and Alphaproteobacteria, specifically Acetobacteraceae, Rhodospirillaceae, Roseiflexaceae, Sphingomonadaceae and Caulobacteraceae families. Mean annual precipitation, pH and available nutrients were the primary factors that shaped AAnPB community structures. The predicted keystone species belonged to the families Acetobacteraceae, Rhodospirillaceae and Sphingomonadanceae. Microcosm experiments demonstrated that inoculation with strains from the three families greatly accelerated the formation and development of BSCs. These observations suggest that AAnPB are likely important functional groups in BSCs that significantly contribute to their formation and important ecosystem services.

Symbiotic Associations in Ascidians: Relevance for Functional Innovation and Bioactive Potential

Associations between different organisms have been extensively described in terrestrial and marine environments. These associations are involved in roles as diverse as nutrient exchanges, shelter or adaptation to adverse conditions. Ascidians are widely dispersed marine invertebrates associated to invasive behaviours. Studying their microbiomes has interested the scientific community, mainly due to its potential for bioactive compounds production-e.g., ET-73 (trabectedin, Yondelis), an anticancer drug. However, these symbiotic interactions embrace several environmental and biological functions with high ecological relevance, inspiring diverse biotechnological applications. We thoroughly reviewed microbiome studies (microscopic to metagenomic approaches) of around 171 hosts, worldwide dispersed, occurring at different domains of life (Archaea, Bacteria, Eukarya), to illuminate the functions and bioactive potential of associated organisms in ascidians. Associations with Bacteria are the most prevalent, namely with Cyanobacteria, Proteobacteria, Bacteroidetes, Actinobacteria and Planctomycetes phyla. The microbiomes of ascidians belonging to Aplousobranchia order have been the most studied. The integration of worldwide studies characterizing ascidians' microbiome composition revealed several functions including UV protection, bioaccumulation of heavy metals and defense against fouling or predators through production of natural products, chemical signals or competition. The critical assessment and characterization of these communities is extremely valuable to comprehend their biological/ecological role and biotechnological potential.

Biochemical unity revisited: microbial central carbon metabolism holds new discoveries, multi-tasking pathways, and redundancies with a reason

For a long time, our understanding of metabolism has been dominated by the idea of biochemical unity, i.e., that the central reaction sequences in metabolism are universally conserved between all forms of life. However, biochemical research in the last decades has revealed a surprising diversity in the central carbon metabolism of different microorganisms. Here, we will embrace this biochemical diversity and explain how genetic redundancy and functional degeneracy cause the diversity observed in central metabolic pathways, such as glycolysis, autotrophic CO2 fixation, and acetyl-CoA assimilation. We conclude that this diversity is not the exception, but rather the standard in microbiology.

Assessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M

Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pangenome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.

Adaptation of Dinoroseobacter shibae to oxidative stress and the specific role of RirA

Dinoroseobacter shibae living in the photic zone of marine ecosystems is frequently exposed to oxygen that forms highly reactive species. Here, we analysed the adaptation of D. shibae to different kinds of oxidative stress using a GeLC-MS/MS approach. D. shibae was grown in artificial seawater medium in the dark with succinate as sole carbon source and exposed to hydrogen peroxide, paraquat or diamide. We quantified 2580 D. shibae proteins. 75 proteins changed significantly in response to peroxide stress, while 220 and 207 proteins were differently regulated by superoxide stress and thiol stress. As expected, proteins like thioredoxin and peroxiredoxin were among these proteins. In addition, proteins involved in bacteriochlophyll biosynthesis were repressed under disulfide and superoxide stress but not under peroxide stress. In contrast, proteins associated with iron transport accumulated in response to peroxide and superoxide stress. Interestingly, the iron-responsive regulator RirA in D. shibae was downregulated by all stressors. A rirA deletion mutant showed an improved adaptation to peroxide stress suggesting that RirA dependent proteins are associated with oxidative stress resistance. Altogether, 139 proteins were upregulated in the mutant strain. Among them are proteins associated with protection and repair of DNA and proteins (e. g. ClpB, Hsp20, RecA, and a thioredoxin like protein). Strikingly, most of the proteins involved in iron metabolism such as iron binding proteins and transporters were not part of the upregulated proteins. In fact, rirA deficient cells were lacking a peroxide dependent induction of these proteins that may also contribute to a higher cell viability under these conditions.

Nutrient Exposure Alters Microbial Composition, Structure, and Mercury Methylating Activity in Periphyton in a Contaminated Watershed

The conversion of mercury (Hg) to monomethylmercury (MMHg) is a critical area of concern in global Hg cycling. Periphyton biofilms may harbor significant amounts of MMHg but little is known about the Hg-methylating potential of the periphyton microbiome. Therefore, we used high-throughput amplicon sequencing of the 16S rRNA gene, ITS2 region, and Hg methylation gene pair (hgcAB) to characterize the archaea/bacteria, fungi, and Hg-methylating microorganisms in periphyton communities grown in a contaminated watershed in East Tennessee (United States). Furthermore, we examined how nutrient amendments (nitrate and/or phosphate) altered periphyton community structure and function. We found that bacterial/archaeal richness in experimental conditions decreased in summer and increased in autumn relative to control treatments, while fungal diversity generally increased in summer and decreased in autumn relative to control treatments. Interestingly, the Hg-methylating communities were dominated by Proteobacteria followed by Candidatus Atribacteria across both seasons. Surprisingly, Hg methylation potential correlated with numerous bacterial families that do not contain hgcAB, suggesting that the overall microbiome structure of periphyton communities influences rates of Hg transformation within these microbial mats. To further explore these complex community interactions, we performed a microbial network analysis and found that the nitrate-amended treatment resulted in the highest number of hub taxa that also corresponded with enhanced Hg methylation potential. This work provides insight into community interactions within the periphyton microbiome that may contribute to Hg cycling and will inform future research that will focus on establishing mixed microbial consortia to uncover mechanisms driving shifts in Hg cycling within periphyton habitats.

Litoreibacter roseus sp. nov., a novel bacteriochlorophyll a-containing bacterium

A strictly aerobic, bacteriochlorophyll (BChl) a-containing alphaproteobacterium, designated strain K6^T, was isolated from seawater around an aquaculture site in the Uwa Sea in Japan. The novel strain grew optimally at 30 °C at pH 7.0-7.5 and in the presence of 2.0 % (w/v) NaCl. The nonmotile and coccoid or rod-shaped cells formed pink-pigmented colonies on agar plates containing organic compounds. Cells showed an in vivo absorption maximum at 870 nm in the near-infrared region, indicating the presence of BChl a in the light-harvesting 1 complex. The new bacterial strain was Gram-stain-negative and oxidase- and catalase-positive. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain K6^T was closely related to species in the genus Litoreibacter. The closest phylogenetic relatives of strain K6^T were Litoreibacter ponti GJSW-31^T (98.56 % sequence similarity), Litoreibacter janthinus KMM 3842^T (97.63 %) and Litoreibacter albidus KMM 3851^T (96.88 %). The G+C content of the genomic DNA was 58.26 mol%. The average nucleotide identity value of strain K6^T with the type strain of L. ponti was 77.16 % (SD 4.79 %). The digital DNA-DNA hybridization value of strain K6^T with the type strain of L. ponti was 19.40 %. The respiratory quinone was ubiquinone-10. The major cellular fatty acids were C_18 : 1 ω7c, C_16 : 0 and 11-methyl C_18 : 1 ω7c. The dominant polar lipids were phosphatidylcholine and phosphatidylglycerol. On the basis of the genetic and phenotypic data obtained in the present study, we propose a new species in the genus Litoreibacter: Litoreibacter roseus sp. nov., whose type strain is K6^T (=DSM 110109^T=NBRC 114114^T). Strain K6^T represents the first confirmed species that produces BChl a within the genus Litoreibacter.

Chemotaxis-selective colonization of mangrove rhizosphere microbes on nine different microplastics

Microplastics pollution poses a new threat to the environment of intertidal zone. The sea forest, mangrove, has been polluted by a large number of plastic debris worldwide. To fill the gaps in knowledge of mangrove rhizosphere microbes connected with the 'plasticsphere', a semi-controlled in situ exposure experiment for nine different types of microplastics were conducted in mangrove ecosystem. A sign of biodegrading was observed on polyethylene, polyamide 6 and polyvinyl chloride microplastics surface after 3 months exposure. We discovered that the metabolic activities of the dominant bacteria on certain microplastics were related to the specific groups on polymers molecule. The selective colonization may be driven by the chemotaxis of bacteria. Specially, microplastics biofilms of polyethylene, polyamide 6, polyvinyl chloride and expanded polystyrene possess distinctive dominant bacteria assemblages which have great significance in ecosystem processes involving carbon cycle or sulfur cycle. Community of mangrove soil microorganism and microplastic biofilm varies as the seasons changes. As a new niche, microplastics has higher inclusivity to bacteria than surrounding soil. Additionally, pathogens for human beings (Vibrio parahaemolyticus and Escherichia-Shigella) were detected both in microplastics and soil. We stress that the interaction between microplastics and rhizosphere microorganisms may affect the growth and health of mangrove plants. Besides, we point out that mangrove rhizosphere microorganism can be an ideal candidate for plastics-degradation.

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.

How Thermodynamics Illuminates Population Interactions in Microbial Communities

In traditional population models of microbial ecology, there are two central players: producers and consumers (including decomposers that depend on organic carbon). Producers support surface ecosystems by generating adenosine triphosphate (ATP) from sunlight, part of which is used to build new biomass from carbon dioxide. In contrast, the productivity of subsurface ecosystems with a limited supply of sunlight must rely on bacteria and archaea that are able generate ATP solely from chemical or electric energy to fix inorganic carbon. These “light-independent producers” are frequently not included in traditional food webs, even though they are ubiquitous in nature and interact with one another through the utilization of the by-products of others. In this review, we introduce theoretical approaches based on population dynamics that incorporate thermodynamics to highlight characteristic interactions in the microbial community of subsurface ecosystems, which may link community structures and ecosystem expansion under conditions of a limited supply of sunlight. In comparison with light-dependent producers, which compete with one another for light, the use of Gibbs free energy (chemical energy) can lead cooperative interactions among light-independent producers through the effects of the relative quantities of products and reactants on the available chemical energy, which is termed abundant resource premium. The development of a population theory that incorporates thermodynamics offers fundamental ecological insights into subsurface microbial ecosystems, which may be applied to fields of study such as environmental science/engineering, astrobiology, or the microbial ecosystems of the early earth.

Photoreduction of carotenoids in the aerobic anoxygenic photoheterotrophs probed by real time Raman spectroscopy

The Aerobic anoxygenic phototrophic bacteria (AAPB) Roseobacter denitrificans and Roseobacter litoralis are widespread in the bacterioplankton community with a particular role in the marine carbon cycle. Measurements of carotenoids isolated from dark-grown cells indicated the presence of spheroidenone (SO, N = 11) and of 3,4 dihydrospheroidenone (N = 10) in the carotenoids isolated from illuminated cells. Time-dependent Raman 514 nm excitation experiments of R. denitrificans and R. litoralis cells grown under illumination demonstrated that v₁ (C=C) of SO exhibits a time-dependent substantial frequency upshift relative to its frequency in the dark-grown cells, in a manner resembling shorting the conjugation length (N). We suggest that the irreversible dark-SO to light- 3,4 dihydrospheroidenone transition observed in the intact carotenoids of R. denitrificans and R. litoralis cells is an operative photoreduction strategy of SO containing AAPB that affects the energy transfer mechanism.

Mixed-culture aerobic anoxygenic photosynthetic bacterial consortia reduce nitrate: Core species dynamics, co-interactions and assessment in raw water of reservoirs

Three consortia of mixed-culture Aerobic Anoxygenic Photosynthetic Bacteria (AAPB) with excellent aerobic denitrifying ability were isolated from drinking water source reservoirs. The results showed that the removal of dissolved organic carbon (DOC) and nitrate nitrogen (NO₃^--N) by mixed-culture AAPB were higher than 90% and 99%, respectively. The Illumina MiSeq sequencing of pufM gene revealed that the dominant genera and their relative abundance changed over the culture periods. Sphingomonas sanxanigenens was the most dominant species observed at 9 h, whereas at 48 h, the most abundant species was Rhodobacter blasticus. A network analysis demonstrated that the co-interactions among the different genera were complex and variable. Mixed-culture AAPB removed more than 30% of NO₃^--N and 25% of DOC from the source water and this study suggests that mixed-culture AAPB can be regarded as a latent denitrifying microbial inoculum in the reservoir raw water treatment.

The Prokaryotic Microbiome of Acropora digitifera is Stable under Short-Term Artificial Light Pollution

Corals harbor a great diversity of symbiotic microorganisms that play pivotal roles in host nutrition, reproduction, and development. Changes in the ocean environment, such as increasing exposure to artificial light at night (ALAN), may alter these relationships and result in a decline in coral health. In this study, we examined the microbiome associated with gravid specimens of the reef-building coral Acropora digitifera. We also assessed the temporal effects of ALAN on the coral-associated microbial community using high-throughput sequencing of the 16S rRNA gene V4 hypervariable region. The A. digitifera microbial community was dominated by phyla Proteobacteria, Firmicutes, and Bacteroidetes. Exposure to ALAN had no large-scale effect on the coral microbiome, although taxa affiliated with Rhodobacteraceae, Caulobacteraceae, Burkholderiaceae, Lachnospiraceae, and Ruminococcaceae were significantly enriched in corals subjected to ALAN. We further noted an increase in the relative abundance of the family Endozoicomonadaceae (Endozoicomonas) as the spawning period approached, regardless of light treatment. These findings highlight the stability of the A. digitifera microbial community under short-term artificial light pollution and provide initial insights into the response of the collective holobiont to ALAN.

Roseobacter cerasinus sp. nov., isolated from a fish farm

An obligate aerobic and bacteriochlorophyll a-containing bacterium, designated strain AI77^T, was isolated from a fish farm in Uwa Sea, Japan. Cells were Gram-stain-negative, coccoid- to oval-shaped, and showed no motility. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain AI77^T is a member of the genus Roseobacter and closely related to Roseobacter ponti MM-7^T (97.8 %), Roseobacter denitrificans OCh 114^T (97.3 %) and Roseobacter litoralis OCh 149^T (97.3 %). The G+C content of strain AI77^T was 61.0 mol%. The average amino acid identity values of the genome in strain AI77^T with those in R. denitrificans OCh 114^T and R. litoralis OCh 149^T were 73.26 % (SD 16.46) and 72.63 % (SD 16.76), respectively. The digital DNA-DNA hybridization values of strain AI77^T with the type strains R. denitrificans OCh 114^T and R. litoralis OCh 149^T were 18.70 and 18.50 %, respectively. The dominant fatty acids (>10 % of total fatty acids) of AI77^T were summed feature 8 (C_18 : 1 ω7c and/or C_18 : 1 ω6c) and saturated fatty acid C_16 : 0. The sole respiratory quinone was ubiquinone-10. The predominant polar lipids were phosphatidylcholine, phosphatidylglycerol and diphosphatidylglycerol. Based on the genetic and phenotypic data obtained herein, we conclude that strain AI77^T represents a new species of the genus Roseobacter, for which we propose the name Roseobacter cerasinus sp. nov.; the type strain is AI77^T (=DSM 110091^T=NBRC 114115^T).

A novel bacterial thiosulfate oxidation pathway provides a new clue about the formation of zero-valent sulfur in deep sea

Zero-valent sulfur (ZVS) has been shown to be a major sulfur intermediate in the deep-sea cold seep of the South China Sea based on our previous work, however, the microbial contribution to the formation of ZVS in cold seep has remained unclear. Here, we describe a novel thiosulfate oxidation pathway discovered in the deep-sea cold seep bacterium Erythrobacter flavus 21–3, which provides a new clue about the formation of ZVS. Electronic microscopy, energy-dispersive, and Raman spectra were used to confirm that E. flavus 21–3 effectively converts thiosulfate to ZVS. We next used a combined proteomic and genetic method to identify thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) playing key roles in the conversion of thiosulfate to ZVS. Stoichiometric results of different sulfur intermediates further clarify the function of TsdA in converting thiosulfate to tetrathionate (⁻O₃S–S–S–SO₃⁻), SoxB in liberating sulfone from tetrathionate to form ZVS and sulfur dioxygenases (SdoA/SdoB) in oxidizing ZVS to sulfite under some conditions. Notably, homologs of TsdA, SoxB, and SdoA/SdoB widely exist across the bacteria including in Erythrobacter species derived from different environments. This strongly indicates that this novel thiosulfate oxidation pathway might be frequently used by microbes and plays an important role in the biogeochemical sulfur cycle in nature.

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.

Polychromatic solar energy conversion in pigment-protein chimeras that unite the two kingdoms of (bacterio)chlorophyll-based photosynthesis

Natural photosynthesis can be divided between the chlorophyll-containing plants, algae and cyanobacteria that make up the oxygenic phototrophs and a diversity of bacteriochlorophyll-containing bacteria that make up the anoxygenic phototrophs. Photosynthetic light harvesting and reaction centre proteins from both kingdoms have been exploited for solar energy conversion, solar fuel synthesis and sensing technologies, but the energy harvesting abilities of these devices are limited by each protein's individual palette of pigments. In this work we demonstrate a range of genetically-encoded, self-assembling photosystems in which recombinant plant light harvesting complexes are covalently locked with reaction centres from a purple photosynthetic bacterium, producing macromolecular chimeras that display mechanisms of polychromatic solar energy harvesting and conversion. Our findings illustrate the power of a synthetic biology approach in which bottom-up construction of photosystems using naturally diverse but mechanistically complementary components can be achieved in a predictable fashion through the encoding of adaptable, plug-and-play covalent interfaces.

Time- and compound-dependent microbial community compositions and oil hydrocarbon degrading activities in seawater near the Chinese Zhoushan Archipelago

Marine microorganisms play an irreplaceable role in removing spilled oil. Zhoushan archipelago has one of the busiest ports and oil stockpiles in China. However, little is known about which and how fast oil-degrading microorganisms could biodegrade spilled oil here. By combining ¹⁴C-/³H-based radiotracer assays and MiSeq sequencing, we report the successive pattern of microbial oil-degrading activities and community compositions. The biodegradation rates of alkanes and PAHs (Polycyclic Aromatic Hydrocarbons) were significantly stimulated by oil addition, and reached their maximum after incubation for 3 and 7 days, respectively. Meanwhile, the abundances of alkB and phnAc genes increased and the bacterial communities continuously shifted. Potential oil-degrading bacteria Alcanivorax, Erythrobacter were the dominant degraders by day 3, whereas the dominant degraders shifted to C1-B045, Alteromonas, Pseudohongiella in the later period. These results provide valuable insights into the cooperative system of the versatile oil-degrading bacteria in successively biodegrading complex oil hydrocarbons in oil spills.

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

The anoxygenic phototrophic bacteria (APB) are an active component of aquatic microbial communities. While DNA-based studies have delivered a detailed picture of APB diversity, they cannot provide any information on the activity of individual species. Therefore, we focused on the expression of a photosynthetic gene by APB communities in two freshwater lakes (Cep lake and the Římov Reservoir) in the Czech Republic. First, we analyzed expression levels of pufM during the diel cycle using RT-qPCR. The transcription underwent a strong diel cycle and was inhibited during the day in both lakes. Then, we compared DNA- (total) and RNA-based (active) community composition by sequencing pufM amplicon libraries. We observed large differences in expression activity among different APB phylogroups. While the total APB community in the Římov Reservoir was dominated by Betaproteobacteria, Alphaproteobacteria prevailed in the active library. A different situation was encountered in the oligotrophic lake Cep where Betaproteobacteria (order Burkholderiales) dominated both the DNA and RNA libraries. Interestingly, in Cep lake we found smaller amounts of highly active uncultured phototrophic Chloroflexi, as well as phototrophic Gemmatimonadetes. Despite the large diversity of APB communities, light repression of pufM expression seems to be a common feature of all aerobic APB present in the studied lakes.

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.

Anoxic growth optimization for metal respiration and photobiological hydrogen production by arsenic-resistant Rhodopseudomonas and Rhodobacter species

The current research focuses on anaerobic respiration of arsenic and other toxic metals by purple nonsulfur bacteria (PNSB). Among the optimization assays performed were carbon utilization, cross metal resistance, and metal respiration, along with a comparison of each assay in photoheterotrophic and chemoheterotrophic growth. The bacteria were identified by the classification of 16S ribosomal RNA gene sequences. Rhodobacter sp. PI3 proved to be more versatile in carbon source utilization (acetate, lactate, citrate, and oxalate), whereas Rhodopseudomonas palustris PI5 proved to be more versatile in metal resistance (arsenate, arsenite, cobalt, lead, selenium, and nickel). Both the strains were found to be positive for photofermentative hydrogen production along with arsenic respiration. This study reveals that anaerobic conditions are more appropriate for better efficiency of PNSB. Our study demonstrates that R. palustris PI5 and Rhodobacter sp. PI3 can be promising candidates for the biohydrogen production along with metal detoxification using heavy metal-polluted effluents as a substrate.

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.

Microbial rhodopsins are major contributors to the solar energy captured in the sea

All known phototrophic metabolisms on Earth rely on one of three categories of energy-converting pigments: chlorophyll-a (rarely -d), bacteriochlorophyll-a (rarely -b), and retinal, which is the chromophore in rhodopsins. While the significance of chlorophylls in solar energy capture has been studied for decades, the contribution of retinal-based phototrophy to this process remains largely unexplored. We report the first vertical distributions of the three energy-converting pigments measured along a contrasting nutrient gradient through the Mediterranean Sea and the Atlantic Ocean. The highest rhodopsin concentrations were observed above the deep chlorophyll-a maxima, and their geographical distribution tended to be inversely related to that of chlorophyll-a. We further show that proton-pumping proteorhodopsins potentially absorb as much light energy as chlorophyll-a-based phototrophy and that this energy is sufficient to sustain bacterial basal metabolism. This suggests that proteorhodopsins are a major energy-transducing mechanism to harvest solar energy in the surface ocean.

Flourishing deep-sea AAP bacteria detected by flow cytometric sorting and molecular analysis

Pigmented bacteria cells, including aerobic anoxygenic phototrophic (AAP) bacteria, contribute significantly to secondary production and aquatic carbon cycling but their distribution in the deep sea is still not well understood, especially in the South China Sea. In this study, microscopic, flow cytometric, and molecular analyses were carried out to investigate the abundance and diversity of AAP bacteria at seven stations in the South China Sea. The results revealed the existence of bacteriochlorophyll-containing bacteria below 500 m from two of seven stations. Flow cytometric analysis detected red and infra-red fluorescence under blue (488 nm) light excitation from fluorescent cells. Blue light-excited red fluorescence of these cells from the 1000 m depth at station E403 were verified using epifluorescence microscopy. Based on fluorescence and side scatter features, fluorescent cells were sorted and subjected to molecular analysis. DNA was extracted from these sorted cells from both stations for PCR amplification using 16S rDNA primers. Sequencing of the PCR products showed that the sorted cells from the 1000 m depth at station E403 belonged to the genus Porphyrobacter. The cell population sorted from 500 m at station E703 contained Sphingomonas and a Methylobacterium-like taxon. All these three taxa belong to aerobic anoxygenic phototrophic alpha-proteobacteria. Using flow cytometric analysis, we found that the abundance of Porphyrobacter sp. at 1000 m was 2.71–2.95×10⁴ cells mL^-1 whereas cell counts of Sphingomonas sp. and Methylobacterium at 500 m were about 3.75–4.12×10⁵ cells mL^-1. These results indicate that albeit not ubiquitous in deep water, bacteriochlorophyll-containing bacteria can be abundant in the deep-sea aphotic zone.

Regulation of the Erythrobacter litoralis DSM 8509 general stress response by visible light

Extracytoplasmic function (ECF) sigma factors are environmentally responsive transcriptional regulators. In Alphaproteobacteria, σ^EcfG activates general stress response (GSR) transcription and protects cells from multiple stressors. A phosphorylation-dependent protein partner switching mechanism, involving HWE/HisKA_2-family histidine kinases, underlies σ^EcfG activation. The identity of these sensor kinases and the signals that regulate them remain largely uncharacterized. We have developed the aerobic anoxygenic photoheterotroph (AAP), Erythrobacter litoralis DSM 8509, as a comparative genetic model to investigate GSR. Using this system, we sought to define the role of visible light and a photosensory HWE kinase, LovK, in regulation of GSR transcription. We identified three HWE kinase genes that collectively control GSR: gsrK and lovK are activators, while gsrP is a repressor. In wild-type cells, GSR transcription is activated in the dark and nearly off in the light, and the opposing activities of gsrK and gsrP are sufficient to modulate GSR transcription in response to illumination. In the absence of gsrK and gsrP, lovK alone is sufficient to activate GSR transcription. lovK is a more robust activator in the dark, and light-dependent regulation by LovK requires that its N-terminal LOV domain be photochemically active. Our studies establish a role for visible light and an ensemble of HWE kinases in light-dependent regulation of GSR transcription in E. litoralis.

Emended description of the genus Tabrizicola and the species Tabrizicola aquatica as aerobic anoxygenic phototrophic bacteria

The genus Tabrizicola with its type species and strain Tabrizicola aquatica RCRI19^T was previously described as a purely chemotrophic genus of Gram-negative, aerobic, non-motile and rod-shaped bacteria. With the present study, we expand the description of the metabolic capabilities of this genus and the T. aquatica type strain to include chlorophyll-dependent phototrophy. Our results confirmed that T. aquatica, does not grow under anaerobic photoautotrophic or photoheterotrophic conditions. However, the presence of the photosynthesis-related genes pufL and pufM could be demonstrated in the genomes of several Tabrizicola strains. Additionally, photosynthetic pigments (bacteriochlorophyll a) were formed under aerobic, heterotrophic and low light conditions in T. aquatica strain RCRI19^T. Furthermore, all the genes necessary for a fully operational photosynthetic apparatus and bacteriochlorophyll a are present in the T. aquatica type strain genome. Therefore, we suggest categorising T. aquatica RCRI19^T, isolated from freshwater environment of Qurugöl Lake, as an aerobic anoxygenic phototrophic (AAP) bacterium.

Complete Genome Sequence of the Marine Carbazole-Degrading Bacterium Erythrobacter sp. Strain KY5

We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium isolated from Tokyo Bay and capable of degrading carbazole.

We determined the complete genome sequence of Erythrobacter sp. strain KY5, a bacterium isolated from Tokyo Bay and capable of degrading carbazole. The genome consists of a 3.3-Mb circular chromosome that carries the gene clusters involved in carbazole degradation and biosynthesis of the photosynthetic apparatus of aerobic anoxygenic phototrophic bacteria.