Search Results (40)

Biological soil crusts (referred to as biocrusts) constitute prominent components within the ecosystem of tropical coral islands in the South China Sea, covering approximately 6.25% of the island’s terrestrial surface. Biocrusts are the key to the restoration of the island ecosystem. It is widely acknowledged that phototrophic microorganisms profoundly contribute to biocrust formation and development. They provide fixed carbon and nitrogen and produce exopolysaccharides for the BSC ecosystems. Although aerobic anoxygenic phototrophic bacteria (AAPB) are an important functional group of phototrophic microorganisms, the community characteristics of AAPB in coral island biocrusts and their role in the formation of biocrusts have rarely been reported. In this study, we employed amplifications of the pufM gene to characterize the AAPB communities of biocrusts on a tropical coral island. The outcomes revealed a discernible augmentation in both the abundance and richness of AAPB concurrent with the formation of biocrusts, concomitantly with a decrement in diversity. Within the AAPB communities, the Pseudomonadota (Proteobacteria) phylum emerges as the prevailing dominion, indicating marked differentiations in terms of family and genus compositions between the biocrust and bare soil. Canonical correlation analysis has unveiled a robust and meaningful correlation between the AAPB composition and the attributes of the soil, including total nitrogen, total organic carbon, total phosphorus, pH, and calcium content. Furthermore, co-occurrence network patterns shift with biocrust formation, enhancing stability. Meanwhile, keystone taxa analysis revealed specific OTUs associated with each soil type, with genus Brevundimonas as the main group. Furthermore, pure-culture AAPB strains isolated from biocrusts exhibited a panorama of diversity, predominantly belonging to Pseudomonadota. Particularly, the Skermanella and Erythrobacter genera demonstrated strong exopolysaccharide secretion and sand-binding capabilities. This study sheds light on the significant functional role of AAPB in tropical coral island biocrusts, expanding our understanding of their contribution to ecosystem services, and providing valuable insights for ecological restoration efforts on coral islands. Full article

Sulfur cycling is a fundamental biogeochemical process, yet its microbial underpinnings in environments like the Isinuka sulfur pool remain poorly understood. Using high-throughput Illumina 16S rRNA sequencing and PICRUSt-based functional inference, we analyzed bacterial diversity and metabolic potential in sediment and water samples. Sediments, characterized by high sulfide/sulfate/thiosulfate, salinity, alkalinity, and organic matter content under anoxic conditions, supported diverse sulfur-reducing and organic-degrading bacteria, primarily from the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria phyla. In contrast, the anoxic water column harbored a less diverse community dominated by α-, γ-, and β-Proteobacteria, including Thiocapsa and Lutimaribacter. Sulfur oxidation genes (soxABCXYZ, sqr) were abundant in water, while sulfate reduction genes (dsrAB, aprAB, and sat/met3) were concentrated in sediments. Core microbiome analysis identified Thiocapsa, Lutimaribacter, and Delftia as functional keystones, integrating sulfur oxidation and nutrient recycling. Sediments supported dissimilatory sulfate-reducing bacteria (unclassified Desulfobacteraceae, Desulfosarcina, Desulfococcus, Desulfotignum, and Desulfobacter), while water samples were enriched in sulfur-oxidizing bacteria like Thiocapsa. Metabolic profiling revealed extensive sulfur, nitrogen, and carbon cycling pathways, with sulfur autotrophic denitrification and anoxygenic photosynthesis coupling sulfur–nitrogen and sulfur–carbon cycles. This study provides key theoretical insights into the microbial dynamics in sulfur-rich environments, highlighting their roles in biogeochemical cycling and potential applications in environmental management. Full article

Through the analysis of core-rim magnetite, we demonstrate that the core contains carbonaceous materials (CMs) derived from a 3.2-billion-year-old banded iron formation within the Barberton Greenstone Belt in South Africa. Using scanning electron microscopy, energy-dispersive X-ray spectroscopy, and Raman spectroscopy, we establish a direct association between these CMs and the magnetite. Although the possibility that CMs formed from the hydrothermal decomposition of siderite cannot be ruled out, several lines of evidence indicate a likely microbial origin for the CMs. Firstly, Raman spectroscopy reveals that the CMs exhibit characteristics of low-maturity biogenic organic matter (OM) featuring aliphatic carbon chains, which supports the notion that organic carbon compounds mature during burial metamorphism at temperatures below approximately 200 °C. Secondly, phosphorus and sulfur detected in the CMs suggest a microbial origin. Lastly, the formation of the unique texture of core-rim magnetite can be conceptualized as follows: Fe²⁺ is oxidized through anoxygenic photosynthesis, leading to the precipitation of ferrihydrite. This ferrihydrite is then transformed into magnetite by iron-reducing microorganisms. Subsequently, the magnetite grows larger through oriented attachment, which also confines OM. Ultimately, smooth magnetite rims may have preserved the OM for up to 3.2 billion years. Full article

Cyanobacteria are widely distributed in natural environments including geothermal areas. A unicellular cyanobacterium, Thermosynechococcus, in a deeply branching lineage, develops thick microbial mats with other bacteria, such as filamentous anoxygenic photosynthetic bacteria in the genus Chloroflexus, in slightly alkaline hot-spring water at ~55 °C. However, Thermosynechococcus strains do not form cell aggregates under axenic conditions, and the cells are dispersed well in the culture. In this study, Thermosynechococcus sp. NK55a and Chloroflexus aggregans NBF, isolated from Nakabusa Hot Springs (Nagano, Japan), were mixed in an inorganic medium and incubated at 50 °C under incandescent light. Small cell aggregates were detected after 4 h incubation, the size of cell aggregates increased, and densely packed cell aggregates (100–200 µm in diameter) developed. Scanning electron microscopy analysis of cell aggregates found that C. aggregans filaments were connected with Thermosynechococcus sp. cells via pili-like fibers. Co-cultivation of C. aggregans with a pili-less mutant of Thermosynechococcus sp. did not form tight cell aggregates. Cell aggregate formation was observed under illumination with 740 nm LED, which was utilized only by C. aggregans. These results suggested that Chloroflexus filaments gather together via gliding motility, and piliated cyanobacterial cells cross-link filamentous cells to form densely packed cell aggregates. Full article

Marshes are an important ecosystem, acting as a biodiversity hotspot, a carbon sink and a bioremediation site, breaking down anthropogenic waste such as antibiotics, metals and fertilizers. Due to their participation in these metabolic activities and their capability to contribute to primary productivity, the microorganisms in such habitats have become of interest to investigate. Since Proteobacteria were previously found to be abundant and the waters are well aerated and organic-rich, this study on the presence of anoxygenic phototrophic bacteria, purple non-sulfur bacteria and aerobic anoxygenic phototrophs in marshes was initiated. One sample was collected at each of the seven Manitoban sites, and anoxygenic phototrophs were cultivated and enumerated. A group of 14 strains, which represented the phylogenetic diversity of the isolates, was physiologically investigated further. Aerobic anoxygenic phototrophs and purple non-sulfur bacteria were present at each location, and they belonged to the α- and β-Proteobacteria subphyla. Some were closely related to known heavy metal reducers (Brevundimonas) and xenobiotic decomposers (Novosphingobium and Sphingomonas). All were able to synthesize the photosynthetic complexes aerobically. This research highlights the diversity of and the potential contributions that anoxygenic phototrophs make to the essential functions taking place in wetlands. Full article

A Type I reaction center (RC) (Fe-S type, ferredoxin reducing) is found in several phyla containing anoxygenic phototrophic bacteria. These include the heliobacteria (HB), the green sulfur bacteria (GSB), and the chloracidobacteria (CB), for which high-resolution homodimeric RC-photosystem (PS) structures have recently appeared. The 2.2-Å X-ray structure of the RC-PS of Heliomicrobium modesticaldum revealed that the core PshA apoprotein (PshA-1 and PshA-2 homodimeric pair) exhibits a structurally conserved PSI arrangement comprising five C-terminal transmembrane α-helices (TMHs) forming the RC domain and six N-terminal TMHs coordinating the light-harvesting (LH) pigments. The Hmi. modesticaldum structure lacked quinone molecules, indicating that electrons were transferred directly from the A₀ (8¹-OH-chlorophyll (Chl) a) acceptor to the F_X [4Fe-4S] component, serving as the terminal RC acceptor. A pair of additional TMHs designated as Psh X were also found that function as a low-energy antenna. The 2.5-Å resolution cryo-electron microscopy (cryo-EM) structure for the RC-PS of the green sulfur bacterium Chlorobaculum tepidum included a pair of Fenna–Matthews–Olson protein (FMO) antennae, which transfer excitations from the chlorosomes to the RC-PS (PscA-1 and PscA-2) core. A pair of cytochromes c_Z (PscC) molecules was also revealed, acting as electron donors to the RC bacteriochlorophyll (BChl) a’ special pair, as well as PscB, housing the [4Fe-4S] cluster F_A and F_B, and the associated PscD protein. While the FMO components were missing from the 2.6-Å cryo-EM structure of the Zn- (BChl) a’ special pair containing RC-PS of Chloracidobacterium thermophilum, a unique architecture was revealed that besides the (PscA)₂ core, consisted of seven additional subunits including PscZ in place of PscD, the PscX and PscY cytochrome c serial electron donors and four low mol. wt. subunits of unknown function. Overall, these diverse structures have revealed that (i) the HB RC-PS is the simplest light–energy transducing complex yet isolated and represents the closest known homolog to a common homodimeric RC-PS ancestor; (ii) the symmetrically localized Ca²⁺-binding sites found in each of the Type I homodimeric RC-PS structures likely gave rise to the analogously positioned Mn₄CaO₅ cluster of the PSII RC and the Tyr_Z RC donor site; (iii) a close relationship between the GSB RC-PS and the PSII Chl proteins (CP)43 and CP47 was demonstrated by their strongly conserved LH-(B)Chl localizations; (iv) LH-BChls of the GSB-RC-PS are also localized in the conserved RC-associated positions of the PSII Chl_Z-D1 and Chl_Z-D2 sites; (v) glycosylated carotenoids of the GSB RC-PS are located in the homologous carotenoid-containing positions of PSII, reflecting an O₂-tolerance mechanism capable of sustaining early stages in the evolution of oxygenic photosynthesis. In addition to the close relationships found between the homodimeric RC-PS and PSII, duplication of the gene encoding the ancestral Type I RC apoprotein, followed by genetic divergence, may well account for the appearance of the heterodimeric Type I and Type II RCs of the extant oxygenic phototrophs. Accordingly, the long-held view that PSII arose from the anoxygenic Type II RC is now found to be contrary to the new evidence provided by Type I RC-PS homodimer structures, indicating that the evolutionary origins of anoxygenic Type II RCs, along with their distinct antenna rings are likely to have been preceded by the events that gave rise to their oxygenic counterparts. Full article

The rates of oxygenic and anoxygenic photosynthesis, the microorganisms responsible for these processes, and the hydrochemical characteristics of the sulfide-containing karst lakes, Black Kichier and Big Kichier (Mari El Republic), were investigated. In these lakes, a plate of anoxygenic phototrophic bacteria (APB) is formed at the upper boundary of sulfide occurrence in the water. The phototrophic community of the chemocline zone was analyzed using a combination of high-throughput sequencing of the 16S rRNA gene fragments and light and electron microscopic techniques. Green-colored Chlorobium clathratiforme were absolutely predominant in both lakes. The minor components included green sulfur bacteria (GSB) Chlorobium spp., symbiotic consortia Chlorochromatium magnum and Pelochromatium roseum, purple sulfur bacteria (PSB) Chromatium okenii, and unidentified phylotypes of the family Chromatiaceae, as well as members of the Chloroflexota: Chloronema sp. and Oscillochloris sp. Based on the results of the molecular analysis, the taxonomic status of Ancalochloris perfilievii and other prosthecate GSB, as well as of the PSB Thiopedia rosea, which were visually revealed in the studied freshwater lakes, is discussed. Full article

Since a large amount of sewage sludge (WSS) is generated daily, exploring effective methods for utilizing WSS is necessary. Although a photo-fermentation system sometimes alters the characteristics of microbial functions, there have been no attempts to perform photo-fermentation using WSS, which is regularly treated via dark fermentation. In this study, the effect of photo-fermentation (photo-irradiation) on anaerobic digestion using WSS was revealed. Photo-irradiation during the anaerobic digestion of WSS significantly reduced the amount of methane and hydrogen sulfide. Methane production was also reduced 5.6-fold at 13 days under light conditions, whereas hydrogen sulfide was consumed almost completely at 6 days. However, it was shown that the activity of sulfate-reducing bacteria in WSS under light treatment increased. Photo-irradiation also stimulated the growth of green sulfur bacteria and induced anoxygenic photosynthesis, via which process the fermented samples turned green in a manner that was correlated with their consumption of hydrogen sulfide. The production of organic acids was lowered in the samples that were irradiated using light. Finally, dark/light switching fermentation was only able to reduce hydrogen sulfide while methane production remained the same. The amounts of methane and hydrogen sulfide were 35 mmol/g VS, and they were undetected at 58 days in photo-irradiated samples compared to the control samples that produced 37 mmol/g VS of methane and 15 ppm/g VS of hydrogen sulfide. Full article

In the pursuit of cultivating anaerobic anoxygenic phototrophs with unusual absorbance spectra, a purple sulfur bacterium was isolated from the shoreline of Baltrum, a North Sea island of Germany. It was designated strain 970, due to a predominant light harvesting complex (LH) absorption maximum at 963–966 nm, which represents the furthest infrared-shift documented for such complexes containing bacteriochlorophyll a. A polyphasic approach to bacterial systematics was performed, comparing genomic, biochemical, and physiological properties. Strain 970 is related to Thiorhodovibrio winogradskyi DSM 6702^T by 26.5, 81.9, and 98.0% similarity via dDDH, ANI, and 16S rRNA gene comparisons, respectively. The photosynthetic properties of strain 970 were unlike other Thiorhodovibrio spp., which contained typical LH absorbing characteristics of 800–870 nm, as well as a newly discovered absorption band at 908 nm. Strain 970 also had a different photosynthetic operon composition. Upon genomic comparisons with the original Thiorhodovibrio strains DSM 6702^T and strain 06511, the latter was found to be divergent, with 25.3, 79.1, and 97.5% similarity via dDDH, ANI, and 16S rRNA gene homology to Trv. winogradskyi, respectively. Strain 06511 (=DSM 116345^T) is thereby described as Thiorhodovibrio litoralis sp. nov., and the unique strain 970 (=DSM 111777^T) as Thiorhodovibrio frisius sp. nov. Full article

This review paper provides an overview of various types of photobioreactors (PBRs) that could be used for the production of polyhydroxyalkanoates (PHAs) using anoxygenic photoheterotrophs, with a focus on the design and operation of these systems. The paper highlights the potential of different PBRs based on reactor geometry and growth mode, and also examines the advantages and disadvantages of each PBR type and summarizes their suitability for PNSB-PHA production. The optimization of reactor design and operation is crucial for maximizing PNSB growth and PHA productivity. The self-immobilization of bacteria in granular sludge is a promising technology for wastewater treatment and the production of PHAs, while grooved-surface PBRs and porous-substrate PBRs have limitations due to difficult biomass harvesting in the former and the presence of aerobic conditions incongruent with PNSB culturing in the latter. Limitations exist with all solutions for maximizing rapid growth and maintaining high biomass concentrations due to the requirements of phototrophic growth. Full article

In this study, we sought to investigate the impact of urbanization, the presence of concrete river bottoms, and nutrient pollution on microbial communities along the L.A. River. Six molecular markers were evaluated for the identification of bacteria, plants, fungi, fish, and invertebrates in 90 samples. PCA (principal components analysis) was used along with PAM (partitioning around medoids) clustering to reveal community structure, and an NB (negative binomial) model in DESeq2 was used for differential abundance analysis. PCA and factor analysis exposed the main axes of variation but were sensitive to outliers. The differential abundance of Proteobacteria was associated with soft-bottom sites, and there was an apparent balance in the abundance of bacteria responsible for nitrogen cycling. Nitrogen cycling was explained via ammonia-oxidizing archaea; the complete ammonia oxidizers, Nitrospira sp.; nitrate-reducing bacteria, Marmoricola sp.; and nitrogen-fixing bacteria Devosia sp., which were differentially abundant at soft-bottom sites (p adj < 0.002). In contrast, the differential abundance of several cyanobacteria and other anoxygenic phototrophs was associated with the impervious sites, which suggested the accumulation of excess nitrogen. The soft-bottom sites tended to be represented by a differential abundance of aerobes, whereas the concrete-associated species tended to be alkaliphilic, saliniphilic, calciphilic, sulfate dependent, and anaerobic. In the Glendale Narrows, downstream from multiple water reclamation plants, there was a differential abundance of cyanobacteria and algae; however, indicator species for low nutrient environments and ammonia-abundance were also present. There was a differential abundance of ascomycetes associated with Arroyo Seco and a differential abundance of Scenedesmaceae green algae and cyanobacteria in Maywood, as seen in the analysis that compared suburban with urban river communities. The proportion of Ascomycota to Basidiomycota within the L.A. River differed from the expected proportion based on published worldwide freshwater and river 18S data; the shift in community structure was most likely associated with the extremes of urbanization. This study indicates that extreme urbanization can result in the overrepresentation of cyanobacterial species that could cause reductions in water quality and safety. Full article

Along the shoreline of the White Sea, due to the post-glacial uplift of the coast, some water bodies with stable stratification have been formed. They have been classified as meromictic as they are at different stages of isolation from the Sea. As separation progresses, significant changes occur in the water column, including the composition of chromophoric dissolved organic matter (CDOM) and the structure of the aquatic microbial community. In this work, we searched for optical proxies of euxinia (anoxic conditions with accumulated hydrogen sulfide) in the water column of the meromictic lagoon on Zeleny Cape. The lagoon is separated from the White Sea basin by a shallow threshold that completely isolates the lagoon during low tide, but marine water enters the lagoon during high tide. The ecosystem in the lagoon is characterized by the marine salinity of water and a high organic matter content in the bottom water and sediments. In this study, spectral methods were used to obtain the depth distribution of CDOM, chlorophyll, and bacteriochlorophyll in the lagoon with strong water stratification and euxinic conditions in the bottom water. The measured optical CDOM characteristics were compared with hydrochemical data (water salinity, Eh, pH, dissolved oxygen), phytoplankton (oxygenic phototrophs), and green sulfur bacteria (anoxygenic phototrophs) distribution along the water column. The spectroscopic methods showed to have the advantages of not requiring water sample pre-treatment and allowing rapid sensing of CDOM and photosynthetic pigments at each horizon. Full article

In natural habitats, bacteria frequently need to adapt to changing environmental conditions. Regulation of transcription plays an important role in this process. However, riboregulation also contributes substantially to adaptation. Riboregulation often acts at the level of mRNA stability, which is determined by sRNAs, RNases, and RNA-binding proteins. We previously identified the small RNA-binding protein CcaF1, which is involved in sRNA maturation and RNA turnover in Rhodobacter sphaeroides. Rhodobacter is a facultative phototroph that can perform aerobic and anaerobic respiration, fermentation, and anoxygenic photosynthesis. Oxygen concentration and light conditions decide the pathway for ATP production. Here, we show that CcaF1 promotes the formation of photosynthetic complexes by increasing levels of mRNAs for pigment synthesis and for some pigment-binding proteins. Levels of mRNAs for transcriptional regulators of photosynthesis genes are not affected by CcaF1. RIP-Seq analysis compares the binding of CcaF1 to RNAs during microaerobic and photosynthetic growth. The stability of the pufBA mRNA for proteins of the light-harvesting I complex is increased by CcaF1 during phototrophic growth but decreased during microaerobic growth. This research underlines the importance of RNA-binding proteins in adaptation to different environments and demonstrates that an RNA-binding protein can differentially affect its binding partners in dependence upon growth conditions. Full article

The bacterium Gemmatimonas phototrophica AP64 isolated from a freshwater lake in the western Gobi Desert represents the first phototrophic member of the bacterial phylum Gemmatimonadota. This strain was originally cultured on agar plates because it did not grow in liquid medium. In contrast, the closely related species G. groenlandica TET16 grows both on solid and in liquid media. Here, we show that the growth of G. phototrophica in liquid medium can be induced by supplementing the medium with 20 mg CaCl₂ L⁻¹. When grown at a lower concentration of calcium (2 mg CaCl₂ L⁻¹) in the liquid medium, the growth was significantly delayed, cells were elongated and lacked flagella. The elevated requirement for calcium is relatively specific as it can be partially substituted by strontium, but not by magnesium. The transcriptome analysis documented that several groups of genes involved in flagella biosynthesis and transport of transition metals were co-activated after amendment of 20 mg CaCl₂ L⁻¹ to the medium. The presented results document that G. phototrophica requires a higher concentration of calcium for its metabolism and growth compared to other Gemmatimonas species. Full article

Aerobic anoxygenic photosynthetic bacteria (AAPB) are a kind of heterotrophic prokaryote that can use bacteriochlorophyll (BChl) for photosynthesis without oxygen production and they are widely distributed in aquatic environments, including oceans, lakes, and rivers. A novel aerobic anoxygenic photosynthetic bacterium strain XJSP^T was isolated during a study of water microbial diversity in Sayram Lake, Xinjiang Province, China. Strain XJSP^T was found to grow optimally at 33 °C, pH 7.5 with 1.0% (w/v) NaCl, and to produce bacteriochlorophyll a and carotenoids. Phylogenetic analysis based on 16S rRNA gene sequence and concatenated alignment sequences of 120 ubiquitous single-copy proteins both supported that strain XJSP^T belonged to the genus Pseudotabrizicola. Both average nucleotide identity (ANI) and DNA–DNA hybridization (DDH) values were below the species delineation threshold. The primary polar lipids were phosphatidylcholine, phosphatidylglycerol, phosphatidylethanolamine, one unknown lipid, and one unidentified phospholipid. Based on the results of polyphasic analyses performed in this study, strain XJSP^T represents a new member of the genus Pseudotabrizicola, for which the name Pseudotabrizicola formosa sp. nov. is proposed. The type strain is XJSP^T (= KCTC 52636^T = MCCC 1H00184^T = SDUM 107003^T). Comparative genomic analysis showed that four species of the genus Pseudotabrizicola shared 2570 core genes and possessed a complete anoxygenic photosystem II. Full article