Nitrogen fixation and nitrogenase activities in members of the family Rhodospirillaceae

Comparative analyses of gut microbiota reveal ammonia detoxification and nitrogen assimilation in Cyprinus carpio var. specularis

The complex niche of fish gut is often characterized by the associated microorganisms that have implications in fish gut-health nexus. Although efforts to distinguish the microbial communities have highlighted their disparate structure along the gut length, remarkably little information is available about their distinct structural and functional profiles in different gut compartments in different fish species. Here, we performed comparative taxonomic and predictive functional analyses of the foregut and hindgut microbiota in an omnivorous freshwater fish species, Cyprinus carpio var. specularis, commonly known as mirror carp. Our analyses showed that the hindgut microbiota could be distinguished from foregut based on the abundance of ammonia-oxidizing, denitrifying, and nitrogen-fixing commensals of families such as Rhodospirillaceae, Oxalobacteraceae, Nitrosomonadaceae, and Nitrospiraceae. Functionally, unique metabolic pathways such as degradation of lignin, 2-nitrobenzoate, vanillin, vanillate, and toluene predicted within hindgut also hinted at the ability of hindgut microbiota for assimilation of nitrogen and detoxification of ammonia. The study highlights a major role of hindgut microbiota in assimilating nitrogen, which remains to be one of the limiting nutrients within the gut of mirror carp.

Relating microbial community composition to treatment performance in an ozone-biologically active carbon filtration potable reuse treatment train

Treatment trains that couple ozone (O3) with biologically active carbon (BAC) filtration are of interest as a lower cost, more sustainable, membrane-free approach to water reuse. However, little is known about the microbial communities that are the fundamental drivers of O3-BAC treatment. The objective of this study was to demonstrate microbial community profiling as a diagnostic tool for assessing the functionality, biological stability, and resilience of coupled physical, chemical, advanced oxidative and biological processes employed in water reuse treatment. We utilized 16S rRNA gene amplicon sequencing to profile the bacterial microbiota over time throughout a potable reuse train employing coagulation, flocculation, sedimentation, ozonation, BAC filtration, granular activated carbon (GAC) adsorption, and UV disinfection. A distinct baseline microbiota was associated with each stage of treatment (ANOSIM, p < 0.05, r-stat = 0.52), each undergoing succession with time and operational shifts. Ozonation resulted in the sharpest shifts (i.e., 83.3 % average change in Genus level relative abundances, when adjusted O3:TOC ratio > 1), and also variance, in microbial community composition. Adjustment in O3:TOC ratios, temperature, filter-aid polymer, monochloramine quenching agent, and empty-bed contact time also resulted in measurable changes in the baseline microbial community composition of individual processes, but to a lesser degree. Of these, supplementation of nitrogen and phosphorus resulted in the strongest bifurcation, especially in the microbial communities inhabiting the BAC (ANOSIM: p < 0.05, BAC5 r-stat = 0.32; BAC10 r-stat = 0.54) and GAC (ANOSIM: p < 0.05, GAC10 r-stat = 0.54; GAC20 r-stat = 0.63) units. Additionally, we found that the BAC microbial community was responsive to an inoculation of microbially active media, which resulted in improved TOC removal. The findings of this study improve understanding of bacterial dynamics occurring in advanced water treatment trains and can inform improved system design and operation.

Metagenomics of two aquifers with thermal anomalies in Mallorca Island, and proposal of new uncultivated taxa named following the rules of SeqCode

Groundwater offers an intriguing blend of distinctive physical and chemical conditions, constituting a challenge for microbial life. In Mallorca, the largest island of Balearic archipelago, harbours a variety of thermal anomalies (i.e., geothermal manifestation where surface aquifers exhibiting temperatures exceeding the regional average). The metagenomes of two aquifers in the centre and southern of the island showed Pseudomonadota to be the most represented phylum when using extracted 16S rRNA gene sequences. However, the microbial structures within and between aquifers were remarkably diverse but similar in their metabolic profiles as revealed by the metagenome-assembled genomes (MAGs) pointing to a prevalence of aerobic chemolithoautotrophic and heterotrophic metabolisms, especially in the Llucmajor aquifer. Also, some evidences of anaerobic lifestyles were detected, which would indicate that these environments either could suffer episodes of oxygen depletion or the anaerobes had been transported from deeper waters. We believe that the local environmental factors (temperature, external inputs or chemistry) seem to be more relevant than the connection and, eventually, transport of microbial cells within the aquifer in determining the highly divergent structures. Notably, most of the reconstructed genomes belonged to undescribed bacterial lineages and from them two high-quality MAGs could be classified as novel taxa named following the rules of the Code for Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). Accordingly, we propose the new species and genus Costitxia debesea gen. nov., sp. nov., affiliated with the novel family Costitxiaceae fam. nov., order Costitxiales ord. nov. and class Costitxiia class. nov.; and the new new species and genus Lloretia debesea gen. nov. sp. nov. affiliated with the novel family Lloretiaceae fam. nov.

The effect of anaerobic digestate as an organic soil fertilizer on the diversity and structure of the indigenous soil microbial and nematode communities

Anaerobic digestate is a popular soil additive which can promote sustainability and transition toward a circular economy. This study addresses how anaerobic digestate modifies soil health when combined with a common chemical fertilizer. Attention was given to soil microbes and, a neglected but of paramount importance soil taxonomic group, soil nematodes. A mesocosm experiment was set up in order to assess the soil's microbial and nematode community. The results demonstrated that the microbial diversity was not affected by the different fertilization regimes, although species richness increased after digestate and mixed fertilization. The composition and abundance of nematode community did not respond to any treatment. Mixed fertilization notably increased potassium (K) and boron (B) levels, while nitrate (NO3-) levels were uniformly elevated across fertilized soils, despite variations in nitrogen input. Network analysis revealed that chemical fertilization led to a densely interconnected network with mainly mutualistic relationships which could cause ecosystem disruption, while digestate application formed a more complex community based on bacterial interactions. However, the combination of both orchestrated a more balanced and less complex community structure, which is more resilient to random disturbances, but on the downside, it is more likely to collapse under targeted perturbations.

Diversity and conservation of the genome architecture of phages infecting the Alphaproteobacteria

IMPORTANCE

This study reports the results of the largest analysis of genome sequences from phages that infect the Alphaproteobacteria class of bacterial hosts. We analyzed over 100 whole genome sequences of phages to construct dotplots, categorize them into genetically distinct clusters, generate a bootstrapped phylogenetic tree, compute protein orthologs, and predict packaging strategies. We determined that the phage sequences primarily cluster by the bacterial host family, phage morphotype, and genome size. We expect that the findings reported in this seminal study will facilitate future analyses that will improve our knowledge of the phages that infect these hosts.

Contrasting response of soil microbiomes to long-term fertilization in various highland cropping systems

Soil microbiomes play important roles in supporting agricultural ecosystems. However, it is still not well-known how soil microbiomes and their functionality respond to fertilization in various cropping systems. Here we examined the effects of 36 years of phosphorus, nitrogen, and manure application on soil bacterial communities, functionality and crop productivity in three contrasting cropping systems (i.e., continuous leguminous alfalfa (AC), continuous winter wheat (WC), and grain-legume rotation of winter wheat + millet - pea - winter wheat (GLR)) in a highland region of China's Loess Plateau. We showed that long-term fertilization significantly affected soil bacterial communities and that the effects varied with cropping system. Compared with the unfertilized control, fertilization increased soil bacterial richness and diversity in the leguminous AC system, whereas it decreased those in the GLR system. Fertilization, particularly manure application, enlarged the differences in soil bacterial communities among cropping systems. Soil bacterial communities were mostly affected by the soil organic carbon and nitrogen contents in the WC and GLR systems, but by the soil available phosphorous content in the AC system. Crop productivity was closely associated with the abundance of fertilization-responsive taxa in the three cropping systems. Our study highlights that legume and non-legume cropping systems should be disentangled when assessing the responses of soil microbial communities to long-term fertilizer application.

Effective combination of arugula vermicompost, chitin and inhibitory bacteria for suppression of the root-knot nematode Meloidogyne javanica and explanation of their beneficial properties based on microbial analysis

Root-knot nematodes (Meloidogyne spp.) are dangerous parasites of many crops worldwide. The threat of chemical nematicides has led to increasing interest in studying the inhibitory effects of organic amendments and bacteria on plant-parasitic nematodes, but their combination has been less studied. One laboratory and four glasshouse experiments were conducted to study the effect on M. javanica of animal manure, common vermicompost, shrimp shells, chitosan, compost and vermicompost from castor bean, chinaberry and arugula, and the combination of arugula vermicompost with some bacteria, isolated from vermicompost or earthworms. The extract of arugula compost and vermicompost, common vermicompost and composts from castor bean and chinaberry reduced nematode egg hatch by 12-32% and caused 13-40% mortality of second-stage juveniles in vitro. Soil amendments with the combination vermicompost of arugula + Pseudomonas. resinovorans + Sphingobacterium daejeonense + chitosan significantly increased the yield of infected tomato plants and reduced nematode reproduction factor by 63.1-76.6%. Comparison of chemical properties showed that arugula vermicompost had lower pH, EC, and C/N ratio than arugula compost. Metagenomics analysis showed that Bacillus, Geodermatophilus, Thermomonas, Lewinella, Pseudolabrys and Erythrobacter were the major bacterial genera in the vermicompost of arugula. Metagenomics analysis confirmed the presence of chitinolytic, detoxifying and PGPR bacteria in the vermicompost of arugula. The combination of arugula vermicompost + chitosan + P. resinovorans + S. daejeonense could be an environmentally friendly approach to control M. javanica.

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

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

Establishment of an unfed strain of Paramecium bursaria and analysis of associated bacterial communities controlling its proliferation

The ciliate Paramecium bursaria harbors several hundred symbiotic algae in its cell and is widely used as an experimental model for studying symbiosis between eukaryotic cells. Currently, various types of bacteria and eukaryotic microorganisms are used as food for culturing P. bursaria; thus, the cultivation conditions are not uniform among researchers. To unify cultivation conditions, we established cloned, unfed strains that can be cultured using only sterile medium without exogenous food. The proliferation of these unfed strains was suppressed in the presence of antibiotics, suggesting that bacteria are required for the proliferation of the unfed strains. Indeed, several kinds of bacteria, such as Burkholderiales, Rhizobiales, Rhodospirillales, and Sphingomonadales, which are able to fix atmospheric nitrogen and/or degrade chemical pollutants, were detected in the unfed strains. The genetic background of the individually cloned, unfed strains were the same, but the proliferation curves of the individual P. bursaria strains were very diverse. Therefore, we selected multiple actively and poorly proliferating individual strains and compared the bacterial composition among the individual strains using 16S rDNA sequencing. The results showed that the bacterial composition among actively proliferating P. bursaria strains was highly homologous but different to poorly proliferating strains. Using unfed strains, the cultivation conditions applied in different laboratories can be unified, and symbiosis research on P. bursaria will make great progress.

Nitrogen Fixation Activity and Genome Analysis of a Moderately Haloalkaliphilic Anoxygenic Phototrophic Bacterium Rhodovulum tesquicola

The genome of the moderately haloalkaliphilic diazotrophic anoxygenic phototrophic bacterium Rhodovulum tesquicola A-36sT isolated from an alkaline lake was analyzed and compared to the genomes of the closest species Rhodovulum steppense A-20sT and Rhodovulum strictum DSM 11289T. The genomic features of three organisms are quite similar, reflecting their ecological and physiological role of facultative photoheterotrophs. Nevertheless, the nitrogenase activity of the pure cultures of the studied bacteria differed significantly: the highest rate (4066 nmoles C2H2/mg of dry weight per hour) was demonstrated by Rhodovulum strictum while the rates in Rhodovulum tesquicola and Rhodovulum steppense were an order of magnitude lower (278 and 523 nmoles C2H2/mg of dry weight per hour, respectively). This difference can be attributed to the presence of an additional nitrogenase operon found exclusively in R. strictum and to the structural variation in nitrogenase operon in R. tesquicola.

Soil Bacterial Community Structure in Different Micro-Habitats on the Tidal Creek Section in the Yellow River Estuary

Tidal creeks have attracted considerable attention in estuary wetland conservation and restoration with diverse micro-habitats and high hydrological connectivity. Bacterial communities act effectively as invisible engines to regulate nutrient element biogeochemical processes. However, few studies have unveiled the bacterial community structures and diversities of micro-habitats soils on the tidal creek section. Our study selected three sections cross a tidal creek with obviously belt-like habitats “pluff mudflat – bare mudflat – Tamarix chinensis community – T. chinensis-Suaeda salsa community– S. salsa community” in the Yellow River estuarine wetland. Based on soil samples, we dissected and untangled the bacterial community structures and special bacterial taxa of different habitats on the tidal creek section. The results showed that bacterial community structures and dominant bacterial taxa were significantly different in the five habitats. The bacterial community diversities significantly decreased with distance away from tidal creeks, as well as the dominant bacteria Flavobacteriia and δ-Proteobacteria, but in reverse to Bacteroidetes and Gemmatimonadetes. Moreover, the important biomarkers sulfate-reducing bacteria and photosynthetic bacteria were different distributions within the five habitats, which were closely associated with the sulfur and carbon cycles. We found that the bacterial communities were heterogeneous in different micro-habitats on the tidal creek section, which was related to soil salinity, moisture, and nutrients as well as tidal action. The study would provide fundamental insights into understanding the ecological functions of bacterial diversities and biogeochemical processes influenced by tidal creeks.

Rhizosphere Diazotrophs and Other Bacteria Associated with Native and Encroaching Legumes in the Succulent Karoo Biome in South Africa

Total and diazotrophic bacteria were assessed in the rhizosphere soils of native and encroaching legumes growing in the Succulent Karoo Biome (SKB), South Africa. These were Calobota sericea, Lessertia diffusa, Vachellia karroo, and Wiborgia monoptera, of Fabaceae family near Springbok (Northern Cape Province) and neighboring refugia of the Fynbos biome for C. sericea for comparison purposes. Metabarcoding approach using 16S rRNA gene revealed Actinobacteria (26.7%), Proteobacteria (23.6%), Planctomycetes, and Acidobacteria (10%), while the nifH gene revealed Proteobacteria (70.3%) and Cyanobacteria (29.5%) of the total sequences recovered as the dominant phyla. Some of the diazotrophs measured were assigned to families; Phyllobacteriaceae (39%) and Nostocaceae (24.4%) (all legumes), Rhodospirillaceae (7.9%), Bradyrhizobiaceae (4.6%) and Methylobacteriaceae (3%) (C. sericea, V. karroo, W. monoptera), Rhizobiaceae (4.2%; C. sericea, L. diffusa, V. Karroo), Microchaetaceae (4%; W. monoptera, V. karroo), Scytonemataceae (3.1%; L. diffusa, W. monoptera), and Pseudomonadaceae (2.7%; V. karroo) of the total sequences recovered. These families have the potential to fix the atmospheric nitrogen. While some diazotrophs were specific or shared across several legumes, a member of Mesorhizobium species was common in all rhizosphere soils considered. V. karroo had statistically significantly higher Alpha and distinct Beta-diversity values, than other legumes, supporting its influence on soil microbes. Overall, this work showed diverse bacteria that support plant life in harsh environments such as the SKB, and shows how they are influenced by legumes.

Potential of Phototrophic Purple Nonsulfur Bacteria to Fix Nitrogen in Rice Fields

Biological nitrogen fixation catalyzed by Mo-nitrogenase of symbiotic diazotrophs has attracted interest because its potential to supply plant-available nitrogen offers an alternative way of using chemical fertilizers for sustainable agriculture. Phototrophic purple nonsulfur bacteria (PNSB) diazotrophically grow under light anaerobic conditions and can be isolated from photic and microaerobic zones of rice fields. Therefore, PNSB as asymbiotic diazotrophs contribute to nitrogen fixation in rice fields. An attempt to measure nitrogen in the oxidized surface layer of paddy soil estimates that approximately 6–8 kg N/ha/year might be accumulated by phototrophic microorganisms. Species of PNSB possess one of or both alternative nitrogenases, V-nitrogenase and Fe-nitrogenase, which are found in asymbiotic diazotrophs, in addition to Mo-nitrogenase. The regulatory networks control nitrogenase activity in response to ammonium, molecular oxygen, and light irradiation. Laboratory and field studies have revealed effectiveness of PNSB inoculation to rice cultures on increases of nitrogen gain, plant growth, and/or grain yield. In this review, properties of the nitrogenase isozymes and regulation of nitrogenase activities in PNSB are described, and research challenges and potential of PNSB inoculation to rice cultures are discussed from a viewpoint of their applications as nitrogen biofertilizer.

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization

BACKGROUND

Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome.

RESULTS

In this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions.

CONCLUSIONS

Standardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.

Niche partitioning of bacterial communities along the stratified water column in the Black Sea

The Black Sea is the largest semi‐closed permanently anoxic basin on our planet with long‐term stratification. The study aimed at describing the Black Sea microbial community taxonomic and functional composition within the range of depths spanning across oxic/anoxic interface, and to uncover the factors behind both their vertical and regional differentiation. 16S rRNA gene MiSeq sequencing was applied to get the data on microbial community taxonomy, and the PICRUSt pipeline was used to infer their functional profile. The normoxic zone was mainly inhabited by primary producers and heterotrophic prokaryotes (e.g., Flavobacteriaceae, Rhodobacteraceae, Synechococcaceae) whereas the euxinic zone—by heterotrophic and chemoautotrophic taxa (e.g., MSBL2, Piscirickettsiaceae, and Desulfarculaceae). Assimilatory sulfate reduction and oxygenic photosynthesis were prevailing within the normoxic zone, while the role of nitrification, dissimilatory sulfate reduction, and anoxygenic photosynthesis increased in the oxygen‐depleted water column part. Regional differentiation of microbial communities between the Ukrainian shelf and offshore zone was detected as well, yet it was significantly less pronounced than the vertical one. It is suggested that regional differentiation within a well‐oxygenated zone is driven by the difference in phytoplankton communities providing various substrates for the prokaryotes, whereas redox stratification is the main driving force behind microbial community vertical structure.

Functional trait relationships demonstrate life strategies in terrestrial prokaryotes

Functional, physiological traits are the underlying drivers of niche differentiation. A common framework related to niches occupied by terrestrial prokaryotes is based on copiotrophy or oligotrophy, where resource investment is primarily in either rapid growth or stress tolerance, respectively. A quantitative trait-based approach sought relationships between taxa, traits and niche in terrestrial prokaryotes. With 175 taxa from 11 Phyla and 35 Families (n = 5 per Family), traits were considered as discrete counts of shared genome-encoded proteins. Trait composition strongly supported non-random functional distributions as preferential clustering of related taxa via unweighted pair-group method with arithmetic mean. Trait similarity between taxa increased as taxonomic rank decreased. A suite of Random Forest models identified traits significantly enriched or depleted in taxonomic groups. These traits conveyed functions related to rapid growth, nutrient acquisition and stress tolerance consistent with their presence in copiotroph-oligotroph niches. Hierarchical clustering of traits identified a clade of competitive, copiotrophic Families resilient to oxidative stress versus glycosyltransferase-enriched oligotrophic Families resistant to antimicrobials and environmental stress. However, the formation of five clades suggested a more nuanced view to describe niche differentiation in terrestrial systems is necessary. We suggest considering traits involved in both resource investment and acquisition when predicting niche.

An overview of anoxygenic phototrophic bacteria and their applications in environmental biotechnology for sustainable Resource recovery

Anoxygenic phototrophic bacteria (APB) are a phylogenetically diverse group of organisms that can harness solar energy for their growth and metabolism. These bacteria vary broadly in terms of their metabolism as well as the composition of their photosynthetic apparatus. Unlike oxygenic phototrophic bacteria such as algae and cyanobacteria, APB can use both organic and inorganic electron donors for light-dependent fixation of carbon dioxide without generating oxygen. Their versatile metabolism, ability to adapt in extreme conditions, low maintenance cost and high biomass yield make APB ideal for wastewater treatment, resource recovery and in the production of high value substances. This review highlights the advantages of APB over algae and cyanobacteria, and their applications in photo-bioelectrochemical systems, production of poly-β-hydroxyalkanoates, single-cell protein, biofertilizers and pigments. The ecology of ABP, their distinguishing factors, various physiochemical parameters governing the production of high-value substances and future directions of APB utilization are also discussed.

Resource availability drives bacterial succession during leaf-litter decomposition in a bromeliad ecosystem

Despite the growing number of investigations on microbial succession during the last decade, most of our knowledge on primary succession of bacteria in natural environments comes from conceptual models and/or studies of chronosequences. Successional patterns of litter-degrading bacteria remain poorly documented, especially in undisturbed environments. Here we conducted an experiment with tank bromeliads as natural freshwater microcosms to assess major trends in bacterial succession on two leaf-litter species incubated with or without animal exclusion. We used amplicon sequencing and a co-occurrence network to assess changes in bacterial community structure according to treatments. Alpha-diversity and community complexity displayed the same trends regardless of the treatments, highlighting that primary succession of detrital-bacteria is subject to resource limitation and biological interactions, much like macro-organisms. Shifts in bacterial assemblages along the succession were characterized by an increase in uncharacterized taxa and potential N-fixing bacteria, the latter being involved in positive co-occurrence between taxa. These findings support the hypothesis of interdependence between taxa as a significant niche-based process shaping bacterial communities during the advanced stage of succession.

Definition of Core Bacterial Taxa in Different Root Compartments of Dactylis glomerata, Grown in Soil under Different Levels of Land Use Intensity

Plant-associated bacterial assemblages are critical for plant fitness. Thus, identifying a consistent plant-associated core microbiome is important for predicting community responses to environmental changes. Our target was to identify the core bacterial microbiome of orchard grass Dactylis glomerata L. and to assess the part that is most sensitive to land management. Dactylis glomerata L. samples were collected from grassland sites with contrasting land use intensities but comparable soil properties at three different timepoints. To assess the plant-associated bacterial community structure in the compartments rhizosphere, bulk soil and endosphere, a molecular barcoding approach based on high throughput 16S rRNA amplicon sequencing was used. A distinct composition of plant-associated core bacterial communities independent of land use intensity was identified. Pseudomonas, Rhizobium and Bradyrhizobium were ubiquitously found in the root bacterial core microbiome. In the rhizosphere, the majority of assigned genera were Rhodoplanes, Methylibium, Kaistobacter and Bradyrhizobium. Due to the frequent occurrence of plant-promoting abilities in the genera found in the plant-associated core bacterial communities, our study helps to identify “healthy” plant-associated bacterial core communities. The variable part of the plant-associated microbiome, represented by the fluctuation of taxa at the different sampling timepoints, was increased under low land use intensity. This higher compositional variation in samples from plots with low land use intensity indicates a more selective recruitment of bacteria with traits required at different timepoints of plant development compared to samples from plots with high land use intensity.

Nitrogen transformation processes and mass balance in deep constructed wetlands treating sewage, exploring the anammox contribution

This work was aimed to assess the contribution of classical nitrogen removal pathways in two deep constructed wetlands CW1 and CW2 located at Jaipur, India. Nitrogen mass balance revealed that 44.87% and 43.77% losses of T-N in CW1 and CW2 were unaccounted for. To elucidate these significant losses, the study was extended to assess the occurrence and contribution of a novel pathway (ANAMMOX) in overall nitrogen removal. The ratio of NH⁴⁺-N (removed) & NO₃^--N (produced) in CW1 & CW2 indicated that ANAMMOX could be one of the key pathways for nitrogen removal in the CWs besides nitrification-denitrification in microbial films. The molecular analysis confirmed bands of ANAMMOX bacteria developed intrinsically. The study revealed that deep wetlands can offer a feasible option for the sustenance of ANAMMOX bacteria and may help develop design parameters for CWs for achieving higherT-N removal withsimilarsurface area as that of conventional wetlands.

Characterization of Chlorella vulgaris (Trebouxiophyceae) associated microbial communities1

Microalgae exhibit extensive potential for counteracting imminent challenges in the nutraceutical, pharmaceutical, and biomaterial sectors, but lack economic viability. Biotechnological systems for contamination control could advance the economic viability of microalgal feedstock, but the selection of suitable strains that sustainably promote microalgal productivity remains challenging. In this study, total diversity in phototrophic Chlorella vulgaris cultures was assessed by amplicon sequencing comparing cultures subjected to five different cultivation conditions. Overall, 12 eukaryotic and 53 prokaryotic taxa were identified; Alphaproteobacteria (36.7%) dominated the prokaryotic and C. vulgaris (97.2%) the eukaryotic community. Despite altering cultivation conditions, 2 eukaryotic and 40 prokaryotic taxa remained stably associated with C. vulgaris; diversity between systems did not significantly differ (P > 0.05). Among those, 20 cultivable taxa were isolated and identified by 16S rDNA sequencing. Subsequently, controlled co-cultures were investigated showing stable associations of C. vulgaris with Sphingopyxis sp. and Pseudomonas sp.. Out-competition of C. vulgaris due to ammonium or phosphate limitation was not observed, despite significantly elevated growth of Sphingopyxis sp. and Tistrella sp.. (P < 0.05). Nevertheless, C. vulgaris growth was impaired by Tistrella sp.. Hence, the study provides a selection of stable indigenous prokaryotes and eukaryotes for artificially tailoring microbial biocenoses. Following a bottom-up approach, it provides a base for controlled co-cultures and thus the establishment of even more complex biocenoses using interkingdom assemblages. Such assemblages can benefit from functional richness for improved nutrient utilization, as well as bacterial load control, which can enhance microalgal feedstock production through improved culture stability and productivity.

Iron-Only and Vanadium Nitrogenases: Fail-Safe Enzymes or Something More?

The enzyme molybdenum nitrogenase converts atmospheric nitrogen gas to ammonia and is of critical importance for the cycling of nitrogen in the biosphere and for the sustainability of life. Alternative vanadium and iron-only nitrogenases that are homologous to molybdenum nitrogenases are also found in archaea and bacteria, but they have a different transition metal, either vanadium or iron, at their active sites. So far alternative nitrogenases have only been found in microbes that also have molybdenum nitrogenase. They are less widespread than molybdenum nitrogenase in bacteria and archaea, and they are less efficient. The presumption has been that alternative nitrogenases are fail-safe enzymes that are used in situations where molybdenum is limiting. Recent work indicates that vanadium nitrogenase may play a role in the global biological nitrogen cycle and iron-only nitrogenase may contribute products that shape microbial community interactions in nature.

Effects of modified nanoscale carbon black on plant growth, root cellular morphogenesis, and microbial community in cadmium-contaminated soil

Previous researches have confirmed that modified nanoscale carbon black (MCB) can decrease the bioavailability of heavy metals in soil and accumulation in plant tissues, resulting in the increase of biomass of plant. However, as a nanoparticle, the effects of MCB on plant cell morphology and microbial communities in Cd-contaminated soil are poorly understood. This study, through greenhouse experiments, investigated the effects of MCB as an amendment for 5 mg·kg^-1 Cd-contaminated soil on plant growth, plant cellular morphogenesis, and microbial communities. Two types of plants, metal-tolerant plant ryegrass (Lolium multiflorum), and hyperaccumulator plant chard (Beta vulgaris L. var. cicla) were selected. The results indicated that adding MCB to Cd-contaminated soil, the dry biomass of shoot ryegrass and chard increased by 1.07 and 1.05 times, respectively, comparing with control group (the treatment without MCB). Meanwhile, the physiological characteristics of plant root denoted that adding MCB reduced the damage caused by Cd to plants. The acid phosphatase activity of soils treated with MBC was higher and the dehydrogenase activity was lower than control group during whole 50 days of incubation, while the urease and catalase activity of soils treated with MBC were higher than control group after 25 days of incubation. When compared with the treatment without MCB, the abundances of nitrogen-functional bacteria (Rhodospirillum and Nitrospira) and phosphorus-functional bacteria (Bradyrhizobium and Flavobacterium) increased but that of nitrogen-functional bacteria, Nitrososphaera, declined. The presence of MCB resulted in increased microbial community abundance by reducing the bioavailability of heavy metals in soil, while increasing the abundance of plants by increasing the amount of available nitrogen in soil. The result of this study suggests that MCB could be applied to the in-situ immobilization of heavy metal in contaminated soils because of its beneficial effects on plants growth, root cellular morphogenesis, and microbial community.

Arsenic respiration and detoxification by purple non-sulphur bacteria under anaerobic conditions

Two arsenic-resistant purple non-sulphur bacteria (PNSB), Q3B and Q3C, were isolated (from industrial contaminated site and paddy fields) and identified by SSU rRNA gene sequencing as Rhodospirillum and Rhodospirillaceae species, respectively. Maximum arsenic reduction by these PNSB was observed in anaerobic conditions. Rhodospirillum sp. Q3B showed 74.92% (v/v) arsenic reduction while Rhodospirillaceae sp. Q3C reduced arsenic up to 76.67% (v/v) in anaerobic conditions. Rhodospirillaceae sp. Q3C was found to contain highest carotenoid content up to 5.6mg·g^-1. Under anaerobic conditions, the isolates were able to respire arsenic in the presence of lactate, citrate, and oxalate. Rhodospirillum sp. Q3B and Rhodospirillaceae sp. Q3C were also found to produce hydrogen gas. Such diverse bacteria can be useful tools for bioremediation purposes. These bacteria can be further exploited and optimized to treat wastewater containing arsenic along with bio-hydrogen production.

Elevated seawater temperature disrupts the microbiome of an ecologically important bioeroding sponge

Bioeroding sponges break down calcium carbonate substratum, including coral skeleton, and their capacity for reef erosion is expected to increase in warmer and more acidic oceans. However, elevated temperature can disrupt the functionally important microbial symbionts of some sponge species, often with adverse consequences for host health. Here, we provide the first detailed description of the microbial community of the bioeroding sponge Cliona orientalis and assess how the community responds to seawater temperatures incrementally increasing from 23°C to 32°C. The microbiome, identified using 16S rRNA gene sequencing, was dominated by Alphaproteobacteria, including a single operational taxonomic unit (OTU; Rhodothalassium sp.) that represented 21% of all sequences. The "core" microbial community (taxa present in >80% of samples) included putative nitrogen fixers and ammonia oxidizers, suggesting that symbiotic nitrogen metabolism may be a key function of the C. orientalis holobiont. The C. orientalis microbiome was generally stable at temperatures up to 27°C; however, a community shift occurred at 29°C, including changes in the relative abundance and turnover of microbial OTUs. Notably, this microbial shift occurred at a lower temperature than the 32°C threshold that induced sponge bleaching, indicating that changes in the microbiome may play a role in the destabilization of the C. orientalis holobiont. C. orientalis failed to regain Symbiodinium or restore its baseline microbial community following bleaching, suggesting that the sponge has limited ability to recover from extreme thermal exposure, at least under aquarium conditions.

Paddy soil microbial communities driven by environment- and microbe-microbe interactions: A case study of elevation-resolved microbial communities in a rice terrace

Rice paddies are a significant source of the greenhouse gas methane, which mainly originates from microbial activity. Methane generation in anaerobic systems involves complex interactions of multiple functional microbial groups. Rice paddies installed in hilly terrain are often terraced, providing multiple quasi-independent plots differing primarily in their elevation up a hillside. This represents an excellent study site to explore the influence of environmental factors on microbial communities and interactions among microbial populations. In this study, we used a combination of geochemical analyses, high-throughput amplicon sequencing, and statistical methods to elucidate these interactions. Sulfate, total nitrogen, total iron, and total organic carbon were determined to be critical factors in steering the ecosystem composition and function. Sulfate-reducing bacteria predominated in the rice terrace microbial communities, and Fe(III)-reducing and methane-oxidizing bacteria were abundant as well. Biotic interactions indicated by co-occurrence network analysis suggest mutualistic interactions among these three functional groups. Paddy-scale methane production may be affected by competition among methanogens and sulfate- and Fe(III)-reducing bacteria, or by direct methane oxidation by methane-oxidizing bacteria.

CAPSULE

Microbial communities were characterized in rice terrace. The environment- and microbe-microbe interactions indicated the mitigation of sulfate and Fe on methane production.

Interaction Between Plant Competition and Rhizospheric Bacterial Community Influence Secondary Succession of Abandoned Farmland on the Loess Plateau of China

Interactions between plant and soil communities have important implication for plant competition, development and succession. In order to explore the internal mechanism behind natural succession of abandoned farmland, we test the effect of plant-soil interaction on plant growth and competitive ability through performing a pot experiment, which included three grasses in different successional stages on the Loess Plateau of China (Setaria viridis, Stipa bungeana, and Bothriochloa ischaemum) in monoculture and all possible two- and three-way combinations, along with a plant-free control pot. The plants were harvested after about 4 months, and the rhizospheric soil was collected. The bacterial communities of the soils were analyzed by high-throughput sequencing of the 16S rRNA gene. Plant competition affected richness of bacterial communities. Proteobacteria and Bacteroidetes were generally higher and Actinobacteria and Acidobacteria were lower in relative abundance in the mixed treatments associated with B. ischaemum. Photosynthetic bacterium, Genus Rhodobacter family Rhodospirillaceae, affected the growth condition and increased the competitive ability of B. ischaemum. Differences in the amounts of soil organic carbon, water-soluble organic carbon and nitrate nitrogen and available phosphorus drove the differences in bacterial communities. Our study has an important significance for understanding the trend of natural succession on the abandoned farmland on the Loess Plateau of China.

Organic Carbon Amendments for Enhanced Biological Attenuation of Trace Organic Contaminants in Biochar-Amended Stormwater Biofilters

This study sought to evaluate how dissolved organic carbon (DOC) affects attenuation of trace organic contaminants (TOrCs) in biochar-amended stormwater biofilters. It was hypothesized that (1) DOC-augmented runoff would demonstrate enhanced TOrC biodegradation and (2) biochar-amended sand bearing DOC-cultivated biofilms would achieve enhanced TOrC attenuation due to sorptive retention and biodegradation. Microcosm and column experiments were conducted utilizing actual runoff, DOC from straw and compost, and a suite of TOrCs. Biodegradation of TOrCs in runoff was more enhanced by compost DOC than straw DOC (particularly for atrazine, prometon, benzotriazole, and fipronil). 16S rRNA gene quantification and sequencing revealed that growth-induced microbial community changes were, among replicates, most consistent for compost-augmented microcosms and least consistent for raw runoff microcosms. Compost DOC most robustly enhanced utilization of TOrCs as carbon substrates, possibly due to higher residual nutrient levels upon TOrC exposure. Sand columns containing just 0.5 wt % biochar maintained sorptive TOrC retention in the presence of compost-DOC-cultivated biofilms, and TOrC removal was further enhanced by biological activity. Overall, these results suggest that coamendment with biochar and compost may robustly enhance TOrC attenuation in stormwater biofilters, a finding of significance for efforts to mitigate the impacts of runoff on water quality.

Application of Bioorganic Fertilizer Significantly Increased Apple Yields and Shaped Bacterial Community Structure in Orchard Soil

Application of bioorganic fertilizers has been reported to improve crop yields and change soil bacterial community structure; however, little work has been done in apple orchard soils where the biological properties of the soils are being degraded due to long-term application of chemical fertilizers. In this study, we used Illumina-based sequencing approach to characterize the bacterial community in the 0-60-cm soil profile under different fertilizer regimes in the Loess Plateau. The experiment includes three treatments: (1) control without fertilization (CK); (2) application of chemical fertilizer (CF); and (3) application of bioorganic fertilizer and organic-inorganic mixed fertilizer (BOF). The results showed that the treatment BOF increased the apple yields by 114 and 67 % compared to the CK and CF treatments, respectively. The treatment BOF also increased the soil organic matter (SOM) by 22 and 16 % compared to the CK and CF treatments, respectively. The Illumina-based sequencing showed that Acidobacteria and Proteobacteria were the predominant phyla and Alphaproteobacteria and Gammaproteobacteria were the most abundant classes in the soil profile. The bacterial richness for ACE was increased after the addition of BOF. Compared to CK and CF treatments, BOF-treated soil revealed higher abundance of Proteobacteria, Alphaproteobacteria and Gammaproteobacteria, Rhizobiales, and Xanthomonadales while Acidobacteria, Gp7, Gp17, and Sphaerobacter were found in lower abundance throughout the soil profile. Bacterial community structure varied with soil depth under different fertilizer treatments, e.g., the bacterial richness, diversity, and the relative abundance of Verruccomicrobia, Candidatus Brocadiales, and Skermanella were decreased with the soil depth in all three treatments. Permutational multivariate analysis showed that the fertilizer regime was the major factor than soil depth in the variations of the bacterial community composition. Two groups, Lysobacter and Rhodospirillaceae, were found to be the significantly increased by the BOF addition and the genus Lysobacter may identify members of this group effective in biological control-based plant disease management and the members of family Rhodospirillaceae had an important role in fixing molecular nitrogen. These results strengthen the understanding of responses to the BOF and possible interactions within bacterial communities in soil that can be associated with disease suppression and the accumulation of carbon and nitrogen. The increase of apple yields after the application of BOF might be attributed to the fact that the application of BOF increased SOM, and soil total nitrogen, and changed the bacterial community by enriching Rhodospirillaceae, Alphaprotreobateria, and Proteobacteria.

Unexpectedly high bacteriochlorophyll a concentrations in neotropical tank bromeliads

The contribution of bacteriochlorophyll a (BChl a) to photosynthetically driven electron transport is generally low in aquatic and terrestrial systems. Here, we provide evidence that anoxygenic bacterial phototrophy is widespread and substantial in water retained by tank bromeliads of a primary rainforest in French Guiana. An analysis of the water extracted from 104 randomly selected tank bromeliads using infrared fluorimetry suggested the overall presence of abundant anoxygenic phototrophic bacterial populations. We found that purple bacteria dominated these populations responsible for unusually high BChl a/chlorophyll a ratios (>50%). Our data suggest that BChl a-based phototrophy in tank bromeliads can have significant effects on the ecology of tank-bromeliad ecosystems and on the carbon and energy fluxes in Neotropical forests.

The Willow Microbiome Is Influenced by Soil Petroleum-Hydrocarbon Concentration with Plant Compartment-Specific Effects

The interaction between plants and microorganisms, which is the driving force behind the decontamination of petroleum hydrocarbon (PHC) contamination in phytoremediation technology, is poorly understood. Here, we aimed at characterizing the variations between plant compartments in the microbiome of two willow cultivars growing in contaminated soils. A field experiment was set-up at a former petrochemical plant in Canada and after two growing seasons, bulk soil, rhizosphere soil, roots, and stems samples of two willow cultivars (Salix purpurea cv. FishCreek, and Salix miyabeana cv. SX67) growing at three PHC contamination concentrations were taken. DNA was extracted and bacterial 16S rRNA gene and fungal internal transcribed spacer (ITS) regions were amplified and sequenced using an Ion Torrent Personal Genome Machine (PGM). Following multivariate statistical analyses, the level of PHC-contamination appeared as the primary factor influencing the willow microbiome with compartment-specific effects, with significant differences between the responses of bacterial, and fungal communities. Increasing PHC contamination levels resulted in shifts in the microbiome composition, favoring putative hydrocarbon degraders, and microorganisms previously reported as associated with plant health. These shifts were less drastic in the rhizosphere, root, and stem tissues as compared to bulk soil, probably because the willows provided a more controlled environment, and thus, protected microbial communities against increasing contamination levels. Insights from this study will help to devise optimal plant microbiomes for increasing the efficiency of phytoremediation technology.

The influence of protozoa with a filtered and non-filtered seawater culture of Tetraselmis sp., and effects to the bacterial and algal communities over 10 days

In this study a filter was used to remove protozoa and its effects on a Tetraselmis sp. culture were evaluated in terms of final total lipid, final total dry weight, cell counts, and both the bacterial and algal communities. The protozoa species observed within this study was identified as Cohnilembus reniformis. It was observed that on the final day no C. reniformis were present in filtered cultures compared to the non-filtered culture which contained 40±3 C. reniformis/mL. The presence of C. reniformis within the culture did not affect the total lipid or the total dry weight recovered, suggesting that Tetraselmis sp. was capable of surviving and growing in the presence of C. reniformis. Overall it is suggested that an 11 μm filter was effective at removing protozoa, though growing a microalgae culture without filtration did not show any significant effect.

Soybean plants modify metal oxide nanoparticle effects on soil bacterial communities

Engineered nanoparticles (ENPs) are entering agricultural soils through land application of nanocontaining biosolids and agrochemicals. The potential adverse effects of ENPs have been studied on food crops and soil bacterial communities separately; however, how ENPs will affect the interacting plant-soil system remains unknown. To address this, we assessed ENP effects on soil microbial communities in soybean-planted, versus unplanted, mesocosms exposed to different doses of nano-CeO2 (0-1.0 g kg(-1)) or nano-ZnO (0-0.5 g kg(-1)). Nano-CeO2 did not affect soil bacterial communities in unplanted soils, but 0.1 g kg(-1) nano-CeO2 altered soil bacterial communities in planted soils, indicating that plants interactively promote nano-CeO2 effects in soil, possibly due to belowground C shifts since plant growth was impacted. Nano-ZnO at 0.5 g kg(-1) significantly altered soil bacterial communities, increasing some (e.g., Rhizobium and Sphingomonas) but decreasing other (e.g., Ensifer, Rhodospirillaceae, Clostridium, and Azotobacter) operational taxonomic units (OTUs). Fewer OTUs decreased from nano-ZnO exposure in planted (41) versus unplanted (85) soils, suggesting that plants ameliorate nano-ZnO effects. Taken together, plants--potentially through their effects on belowground biogeochemistry--could either promote (i.e., for the 0.1 g kg(-1) nano-CeO2 treatment) or limit (i.e., for the 0.5 g kg(-1) nano-ZnO treatment) ENP effects on soil bacterial communities.

Anaerobic phototrophic nitrite oxidation by Thiocapsa sp. strain KS1 and Rhodopseudomonas sp. strain LQ17

In anaerobic enrichment cultures for phototrophic nitrite-oxidizing bacteria from different freshwater sites, two different cell types, i.e. non-motile cocci and motile, rod-shaped bacteria, always outnumbered all other bacteria. Most-probable-number (MPN) dilution series with samples from two freshwater sites yielded only low numbers (≤3×103 cm−3) of phototrophic nitrite oxidizers. Slightly higher numbers (about 104 cm−3) were found in activated sewage sludge. Anaerobic phototrophic oxidation of nitrite was studied with two different isolates, the phototrophic sulfur bacterium strain KS1 and the purple nonsulfur bacterium strain LQ17, both of which were isolated from activated sludge collected from the municipal sewage treatment plant in Konstanz, Germany. Strain KS1 converted 1 mM nitrite stoichiometrically to nitrate with concomitant formation of cell matter within 2–3 days, whereas strain LQ17 oxidized only up to 60 % of the given nitrite to nitrate within several months with the concomitant formation of cell biomass. Nitrite oxidation to nitrate was strictly light-dependent and required the presence of molybdenum in the medium. Nitrite was oxidized in both the presence and absence of oxygen. Nitrite inhibited growth at concentrations higher than 2 mM. Hydroxylamine and hydrazine were found to be toxic to the phototrophs in the range 5–50 μM and did not stimulate phototrophic growth. Based on morphology, substrate-utilization pattern, in vivo absorption spectra, and 16S rRNA gene sequence similarity, strain KS1 was assigned to the genus Thiocapsa and strain LQ17 to the genus Rhodopseudomonas. Also, Thiocapsa roseopersicina strains DSM 217 and DSM 221 were found to oxidize nitrite to nitrate with concomitant growth. We conclude that the ability to use nitrite phototrophically as electron donor is widespread in nature, but low MPN counts indicate that its contribution to nitrite oxidation in the studied habitats is rather limited.

Identity and dynamics of putative N2 -fixing picoplankton in the Baltic Sea proper suggest complex patterns of regulation

Heterocystous filamentous cyanobacteria are regarded as the main N2 -fixing organisms (diazotrophs) in the Baltic Sea. However, some studies indicate that picoplankton may also be important. The aim of this study was to examine the composition of putative diazotrophs in the picoplankton (< 3 µm) and to identify links to environmental factors. Nitrogenase (nifH) genes were amplified from community DNA by nested PCR, followed by cloning and sequencing. Clone libraries from nine environmental samples collected from the central Baltic Sea (April-October 2003, 3 m depth) and a negative control yielded a total of 433 sequences with an average clone library coverage of 92%. The sequences fell within nifH Clusters I, II and III and formed 15 distinct groups (> 96% amino acid similarity). Most of the sequences (77%) fell into nifH Cluster I (cyanobacteria and α-, β- and γ-Proteobacteria). However, only 26 sequences were related to cyanobacteria (e.g. Pseudanabaena) and among these no unicellular phylotypes were found. Sequences clustering with alternative nitrogenases (anfH) and Archaea were found in one sample while sequences related to anaerobic phylotypes were found in six samples distributed throughout the season. The identified phylogenetic groups showed covariance with several environmental factors but no strong links could be established. This suggests a variable and complex regulation of diazotrophic groups within Baltic Sea picoplankton.

An outer membrane protein A (ompA) homologue from the photosynthetic purple sulfur bacterium Allochromatium vinosum

A 991 bp DNA fragment, consisting of a 225 amino acid reading frame homologous to outer membrane protein coding ompA gene, was cloned from a purple sulfur bacterium Allochromatium vinosum. The homology analysis revealed up to 51% similarity to other bacterial species. The absence of branching within diazotrophs or other taxonomically related groups shows the structural importance of the protein regardless of the metabolism and evolution of the species.

Thiocapsa imhoffii, sp. nov., an alkaliphilic purple sulfur bacterium of the family Chromatiaceae from Soap Lake, Washington (USA)

An alkaliphilic purple sulfur bacterium, strain SC5, was isolated from Soap Lake, a soda lake located in east central Washington state (USA). Cells of strain SC5 were gram-negative, non-motile, and non-gas vesiculate cocci, often observed in pairs or tetrads. In the presence of sulfide, elemental sulfur was deposited internally. Liquid cultures were pink to rose red in color. Cells contained bacteriochlorophyll a and spirilloxanthin as major photosynthetic pigments. Internal photosynthetic membranes were of the vesicular type. Optimal growth of strain SC5 occurred in the absence of NaCl (range 0-4%), pH 8.5 (range pH 7.5-9.5), and 32 degrees C. Photoheterotrophic growth occurred in the presence of sulfide or thiosulfate with only a limited number of organic carbon sources. Growth factors were not required, and cells could fix N2. Dark, microaerobic growth occurred in the presence of both an organic carbon source and thiosulfate. Sulfide and thiosulfate served as electron donors for photoautotrophy, which required elevated levels of CO2. Phylogenetic analysis placed strain SC5 basal to the clade of the genus Thiocapsa in the family Chromatiaceae with a 96.7% sequence similarity to its closest relative, Thiocapsa roseopersicina strain 1711T (DSM217T). The unique assemblage of physiological and phylogenetic properties of strain SC5 defines it as a new species of the genus Thiocapsa, and we describe strain SC5 herein as Tca. imhoffii, sp. nov.

Evidence for limited species diversity of bacteriochlorophyll b-containing purple nonsulfur anoxygenic phototrophs in freshwater habitats

Thirteen new isolates of bacteriochlorophyll b-containing purple nonsulfur bacteria were isolated from four freshwater habitats using specific enrichment methods including the use of long wavelength filters and extincting dilution of the inoculum. The new isolates were compared with the type strain of Blastochloris viridis, strain DSM 133(T), as regards pigments, morphology, carbon nutrition, and phylogeny. All new isolates were budding bacteria, and phototrophic mass cultures were green, brown, or brown-green in color. The pattern of carbon sources photocatabolized were similar in all strains; however, sugars, both mono- and disaccharides, were widely used by the new isolates while they did not support growth of strain DSM 133(T). Phylogenetic analysis showed all new strains to cluster tightly with the type strain with the exception of one brown-colored strain and a mildly thermophilic strain. The results suggest that in contrast to purple nonsulfur bacteria containing bacteriochlorophyll a, those containing bacteriochlorophyll b may not be morphologically or phylogenetically diverse, and group into a tight phylogenetic clade distinct from all other anoxygenic phototrophs.

The phylogeny of purple bacteria: the alpha subdivision

The technique of oligonucleotide cataloging shows the purple photosynthetic eubacteria to comprise three major subdivisions, temporarily called alpha, beta, and gamma--previously designated groups I-III by Gibson et al. (1979). Each subdivision contains a number of non-photosynthetic genera in addition to the photosynthetic ones. The alpha subdivision, the subject of the present report, contains most but not all of the species that fall into the classically defined genera Rhodospirillum, Rhodopseudomonas and Rhodomicrobium. Intermingled with these are a variety of non-photosynthetic species from genera such as Agrobacterium, Rhizobium, Azospirillum, Nitrobacter, Erythrobacter, Phenylobacterium, Aquaspirillum, and Paracoccus. The phylogenetic substructure of the alpha subdivision is presented and the evolutionary significance of the admixture of biochemical phenotypes is discussed.

Regulation of nitrogenase in the photosynthetic bacteriumRhodobacter sphaeroidescontainingdraTGandnifHDKgenes fromRhodobacter capsulatus

The photosynthetic bacteria Rhodobacter capsulatus and Rhodospirillum rubrum regulate their nitrogenase activity by the reversible ADP-ribosylation of nitrogenase Fe-protein in response to ammonium addition or darkness. This regulation is mediated by two enzymes, dinitrogenase reductase ADP-ribosyl transferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). Recently, we demonstrated that another photosynthetic bacterium, Rhodobacter sphaeroides, appears to have no draTG genes, and no evidence of Fe-protein ADP-ribosylation was found in this bacterium under a variety of growth and incubation conditions. Here we show that four different strains of Rba. sphaeroides are incapable of modifying Fe-protein, whereas four out of five Rba. capsulatus strains possess this ability. Introduction of Rba. capsulatus draTG and nifHDK (structural genes for nitrogenase proteins) into Rba. sphaeroides had no effect on in vivo nitrogenase activity and on nitrogenase switch-off by ammonium. However, transfer of draTG from Rba. capsulatus was sufficient to confer on Rba. sphaeroides the ability to reversibly modify the nitrogenase Fe-protein in response to either ammonium addition or darkness. These data suggest that Rba. sphaeroides, which lacks DRAT and DRAG, possesses all the elements necessary for the transduction of signals generated by ammonium or darkness to these proteins.Key words: nitrogenase regulation, nitrogenase modification, photosynthetic bacteria.

Membrane localization, topology, and mutual stabilization of the rnfABC gene products in Rhodobacter capsulatus and implications for a new family of energy-coupling NADH oxidoreductases

The rnf genes in Rhodobacter capsulatus are unique nitrogen fixation genes that encode potential membrane proteins (RnfA, RnfD, and RnfE) and potential iron-sulfur proteins (RnfB and RnfC). In this study, we first analyzed the localization and topology of the RnfA, RnfB, and RnfC proteins. By activity and immunoblot analysis of expression of translational fusions to Escherichia coli alkaline phosphatase, RnfA protein was shown to span the chromatophore membrane with its odd-numbered hydrophilic regions exposed to periplasm. By alkaline treatment of membrane fractions and following immunoblot analysis using antibodies against recombinant proteins expressed in E. coli, both RnfB and RnfC proteins were revealed to situate at the periphery of the chromatophore membranes. Second, mutual interaction of the Rnf proteins was analyzed by immunochemical determinations of RnfB and RnfC proteins in rnf mutants and their complemented derivatives. The contents in cellular fractions indicated that RnfB and RnfC stabilize each other and that the presence of RnfA is necessary for stable existence of both proteins. These results support a hypothesis that the Rnf products are subunits of a membrane complex. Finally, we detected homologs of rnf genes in Haemophilus influenzae and Vibrio alginolyticus by data base searches and in E. coli by cloning of a fragment of an rnfA homolog followed by a data base search. Close comparisons revealed that RnfC has potential binding sites for NADH and FMN which are similar to those found in proton-translocating NADH:quinone oxidoreductases and that RnfA, RnfD, and RnfE show similarity to subunits of sodium-translocating NADH:quinone oxidoreductases. We predict that the putative Rnf complex represents a novel family of energy-coupling NADH oxidoreductases.

Nitrogen fixation by the thermophilic green sulfur bacterium Chlorobium tepidum

The thermophilic green sulfur bacterium Chlorobium tepidum grew with N2, NH4+, or glutamine as the sole nitrogen source under phototrophic (anaerobic-light) conditions. Growth on N2 required increased buffering capacity to stabilize uncharacterized pH changes that occurred during diazotrophic growth. Increased sulfide levels were stimulatory for growth on N2. Levels of nitrogenase activity (acetylene reduction) in N2-grown C. tepidum cells were very high, among the highest ever reported for anoxygenic phototrophic bacteria. Maximal acetylene reduction rates in C. tepidum cells were observed at 48 to 50 degrees C, which is about 15 degrees C higher than the optimum temperature for nitrogenase activity in mesophilic chlorobia, and nitrogenase activity in C. tepidum responded to addition of ammonia by a "switch-off/switch-on" mechanism like that in phototrophic purple bacteria. C. tepidum cells assimilated ammonia mainly via the glutamine synthetase-glutamate synthase pathway, elevated levels of both of these enzymes being present in cells grown on N2. These results show that N2 fixation can occur in green sulfur bacteria up to at least 60 degrees C and that regulatory mechanisms important in control of nitrogenase activity in mesophilic anoxygenic phototrophs also appear to regulate thermally active forms of the enzyme.