Autotrophic, sulfur-oxidizing actinobacteria in acidic environments

Taxonomic diversity of microbial communities in the cold sulfur spring Bezymyanny (Pribaikalsky district, Republic of Buryatia)

The environmental conditions of cold sulfur springs favor the growth and development of abundant and diverse microbial communities with many unique sulfur cycle bacteria. In this work, the taxonomic diversity of microbial communities of three different biotopes (microbial mat, bottom sediment, and water) in the cold sulfur spring Bezymyanny located on the shore of Lake Baikal (Pribaikalsky district, Republic of Buryatia) was studied using high-throughput sequencing of the 16S rRNA gene. By sequencing the microbial mat, bottom sediment, and water samples, 76,972 sequences assigned to 1,714 ASVs (ASV, amplicon sequence variant) were obtained. Analysis of the ASV distribution by biotopes revealed a high percentage (66-93 %) of uniqueness in the three communities studied. An estimate of the alpha diversity index showed that bottom sediment community had higher indices, while microbial mat community was characterized by a lowest diversity. Bacteria of the phyla Pseudomonadota, Bacteroidota, Campylobacterota, Actinomycetota, Desulfobacterota dominated in different proportions in the studied communities. The features of the community structure of the studied biotopes were established. The microbial mat community was represented mainly by Thiothrix (43.2 %). The bottom sediment community was based on Sulfurovum (11.2 %) and co-dominated by unclassified taxa (3.2-1 %). Sequences assigned to the genera Novosphingobium, Nocardioides, Legionella, Brevundimonas, Sphingomonas, Bacillus, Mycobacterium, Sphingopyxis, Bradyrhizobium and Thiomicrorhabdus were found only in the water microbial community. Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were identified in all the communities studied, which indicates the ongoing processes of the sulfur cycle in the Bezymyanny spring ecosystem. It should be noted that sequences of unclassified and uncultivated sulfur cycle bacteria were present in all communities and a significant proportion of sequences (20.3-53.9 %) were not classified.

Microbial Cycling of Sulfur and Other Redox-Sensitive Elements in Porewaters of San Clemente Basin, California, and Cocos Ridge, Costa Rica

The microbial recycling of organic matter in marine sediments depends upon electron acceptors that are utilized based on availability and energetic yield. Since sulfate is the most abundant oxidant once oxygen has been depleted, the sulfide produced after sulfate reduction becomes an important electron donor for autotrophic microbes. The ability of sulfide to be re-oxidized through multiple metabolic pathways and intermediates with variable oxidation states prompts investigation into which species are preferentially utilized and what are the factors that determine the fate of reduced sulfur species. Quantifying these sulfur intermediates in porewaters is a critical first step towards achieving a more complete understanding of the oxidative sulfur cycle, yet this has been accomplished in very few studies, none of which include oligotrophic sedimentary environments in the open ocean. Here we present profiles of porewater sulfur intermediates from sediments underlying oligotrophic regions of the ocean, which encompass about 75% of the ocean's surface and are characterized by low nutrient levels and productivity. Aiming at addressing uncertainties about if and how sulfide produced by the degradation of scarce sedimentary organic matter plays a role in carbon fixation in the sediment, we determine depth profiles of redox-sensitive metals and sulfate isotope compositions and integrate these datasets with 16S rRNA microbial community composition data and solid-phase sulfur concentrations. We did not find significant correlations between sulfur species or trace metals and specific sulfur cycling taxa, which suggests that microorganisms in pelagic and oxic sediments may be generalists utilizing flexible metabolisms to oxidize organic matter through different electron acceptors.

Reversed oxidative TCA (roTCA) for carbon fixation by an Acidimicrobiia strain from a saline lake

Acidimicrobiia are widely distributed in nature and suggested to be autotrophic via the Calvin-Benson-Bassham (CBB) cycle. However, direct evidence of chemolithoautotrophy in Acidimicrobiia is lacking. Here, we report a chemolithoautotrophic enrichment from a saline lake, and the subsequent isolation and characterization of a chemolithoautotroph, Salinilacustristhrix flava EGI L10123T, which belongs to a new Acidimicrobiia family. Although strain EGI L10123T is autotrophic, neither its genome nor Acidimicrobiia metagenome-assembled genomes from the enrichment culture encode genes necessary for the CBB cycle. Instead, genomic, transcriptomic, enzymatic, and stable-isotope probing data hinted at the activity of the reversed oxidative TCA (roTCA) coupled with the oxidation of sulfide as the electron donor. Phylogenetic analysis and ancestral character reconstructions of Acidimicrobiia suggested that the essential CBB gene rbcL was acquired through multiple horizontal gene transfer events from diverse microbial taxa. In contrast, genes responsible for sulfide- or hydrogen-dependent roTCA carbon fixation were already present in the last common ancestor of extant Acidimicrobiia. These findings imply the possibility of roTCA carbon fixation in Acidimicrobiia and the ecological importance of Acidimicrobiia. Further research in the future is necessary to confirm whether these characteristics are truly widespread across the clade.

Bioleaching of polymetallic sulphidic mining residues: influence of increasing solid concentration on microbial community dynamics and metal dissolution

Within the European research project NEMO, a bioleaching strategy was developed for efficient metal extraction from bioleach residue currently heap-leached at Sotkamo (Finland) that still contains sulphidic minerals and valuable metals (Ni, Zn, Co, Cu). The strategy of gradually increasing the solid content with 5% steps allowed the adaptation of the consortium up to 20% (w/w) solid content, with efficient metal dissolution and same dominant bacteria. Largest proportions of Sulfobacillusthermosulfidooxidans while Eh increased suggested it to be most involved in iron oxidation. Acidithiobacilluscaldus was rather found when pH stabilized, in line with a production of protons from sulphur oxidation that maintained low pH. 'Acidithiomicrobium' P2 was favoured towards the end of the runs and at 20% (w/w) solids possibly due to its tolerance to Ni. The use of gene abundance to evaluate biomass in the pulp provided complementary results to classical cell counts in the liquid phase, and suggested a key role of bacteria associated to mineral particles in iron oxidation. Scaling-up in 21-L stirred-tank reactor at 20% (w/w) solids had no detrimental effect on bioleaching and confirmed metal extraction rates. 'Acidithiomicrobium' P2 and Sb. thermosulfidooxidans remained main actors. However, the biological activity was considerably reduced at 30% (w/w) solid concentration, which may be due to a too drastic environmental change for the bacteria to adapt to higher solid concentration. Efficient bioleaching of Sotkamo bioleaching residue at high solid concentration was demonstrated, as well as the robustness of the selected moderately thermophilic consortium, at laboratory and pilot scales.

Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole

The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.

Diversity, distribution and organic substrates preferences of microbial communities of a low anthropic activity cave in North-Western Romania

Introduction

Karst caves are characterized by relatively constant temperature, lack of light, high humidity, and low nutrients availability. The diversity and functionality of the microorganisms dwelling in caves micro-habitats are yet underexplored. Therefore, in-depth investigations of these ecosystems aid in enlarging our understanding of the microbial interactions and microbially driven biogeochemical cycles. Here, we aimed at evaluating the diversity, abundance, distribution, and organic substrate preferences of microbial communities from Peștera cu Apă din Valea Leșului (Leșu Cave) located in the Apuseni Mountains (North-Western Romania).

Materials and Methods

To achieve this goal, we employed 16S rRNA gene amplicon sequencing and community-level physiological profiling (CLPP) paralleled by the assessment of environmental parameters of cave sediments and water.

Results and Discussion

Pseudomonadota (synonym Proteobacteria) was the most prevalent phylum detected across all samples whereas the abundance detected at order level varied among sites and between water and sediment samples. Despite the general similarity at the phylum-level in Leșu Cave across the sampled area, the results obtained in this study suggest that specific sites drive bacterial community at the order-level, perhaps sustaining the enrichment of unique bacterial populations due to microenvironmental conditions. For most of the dominant orders the distribution pattern showed a positive correlation with C-sources such as putrescine, γ-amino butyric acid, and D-malic acid, while particular cases were positively correlated with polymers (Tween 40, Tween 80 and α-cyclodextrin), carbohydrates (α-D-lactose, i-erythritol, D-mannitol) and most of the carboxylic and ketonic acids. Physicochemical analysis reveals that sediments are geochemically distinct, with increased concentration of Ca, Fe, Al, Mg, Na and K, whereas water showed low nitrate concentration. Our PCA indicated the clustering of different dominant orders with Mg, As, P, Fe, and Cr. This information serves as a starting point for further studies in elucidating the links between the taxonomic and functional diversity of subterranean microbial communities.

Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake

Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.

Recent Differentiation of Aquatic Bacterial Communities in a Hydrological System in the Cuatro Ciénegas Basin, After a Natural Perturbation

Pozas Rojas is a hydrological system comprising nine isolated shallow ponds and a deep lagoon, which were temporally merged in 2010 by increased rainfall due to a tropical cyclone. In this work, we assess which components, biotic interactions, or environment filtering effects, drive the assembly of microbial communities after a natural perturbation. Arsenic, pH, and temperature are among the most significant environmental variables between each pond, clustering the samples in two main groups, whereas microbial composition is diverse and unique to each site, with no core at the operational taxonomic unit level and only 150 core genera when studied at the genus level. Los Hundidos lagoon has the most differentiated community, which is highly similar to the epipelagic Mediterranean Sea communities. On the other hand, the shallow ponds at the Pozas Rojas system resemble more to epicontinental hydrological systems, such as some cold rivers of the world and the phreatic mantle from Iowa. Overall, despite being a sole of water body 2 years prior to the sampling, interspecific interactions, rather than environmental selection, seem to play a more important role in Pozas Rojas, bolstered by founder effects on each poza and subsequent isolation of each water body.

Changes in microbial community diversity, composition, and functions upon nitrate and Cr(VI) contaminated groundwater

With the increasing occurrences of nitrate and Cr(VI) pollution globally, microbially driven pollutant reduction and its interaction effects were of growing interest. Despite the increasing number of experimental reports on the simultaneous reduction of nitrate and Cr(VI), a broad picture of the keystone species and metabolic differences in this process remained elusive. This study explored the changing of microorganisms with the introduction of Cr(VI)/NO₃^- through analyzing 242 samples from the NCBI database. The correlation between microbial abundance and environmental factors showed that, the types of energy substances and pollutants species in the environment had an impact on the diversity of microorganisms and community structure. The genus of Zoogloea, Candidatus Accumulibacter, and Candidatus Kapabacteria sp. 59-99 had the ability of denitrification, while genus of Alcaligenes, Kerstersia, Petrimonas, and Leucobacter showed effectively Cr(VI) resistance and reducing ability. Azoarcus, Pseudomonas, and Thauera were recognized as important candidates in the simultaneous reduction of nitrate and Cr(VI). Metagenomic predictions of these microorganisms using PICRUSt2 further highlighted the enrichment of Cr(VI)and nitrate reduction-related genes (such as chrA and norC). Special attention should therefore be paid to these bacteria in subsequent studies to evaluate their performance and mechanisms involved in simultaneous denitrification and chromium removal. The microbial co-occurrence network analysis conducted on this basis emphasized a strong association between community collaboration and pollution removal. Collectively, either site surveys or laboratory experiments, subsequent studies should focus on these microbial populations and the interspecific collaborations as they strongly influence the occurrence of simultaneous nitrate and Cr(VI) reduction.

Composition and functional profiles of microbial communities in two geochemically and mineralogically different caves

Microbial communities in cave ecosystems have specific survival strategies, which is far from being well explicated. Here, we reported the genetic and functional diversity of bacteria and archaea in typical limestone (Kashmir Cave) and silicate-containing (Tiser Cave) caves. X-ray diffraction (XRD) and Fourier transform infrared spectroscopic (FTIR) analyses revealed the different geochemical and mineral compositions of the two caves. Amplicon barcode sequencing revealed the dominancy of Actinobacteria and Proteobacteria in Kashmir and Tiser Caves. Bacteroidetes and Firmicutes were the dominant phyla in Tiser Cave, and the abundance is relatively small in Kashmir Cave. Archaea was also abundant prokaryotes in Kashmir Cave, but it only accounted for 0.723% of the total prokaryote sequences in Tiser Cave. Functional analysis based on metagenomic sequencing data revealed that a large number of functional potential genes involved in nutrient metabolism and biosynthesis of bioactive compounds in Tiser and Kashmir Cave samples could significantly influence the biogeochemical cycle and secondary metabolite production in cave habitats. In addition, the two caves were also found to be rich in biosynthetic genes, encoding bioactive compounds, such as monobactam and prodigiosin, indicating that these caves could be potential habitats for the isolation of antibiotics. This study provides a comprehensive insight into the diversity of bacteria and archaea in cave ecosystems and helps to better understand the special survival strategies of microorganisms in cave ecosystems.Key points• Geochemically distinct caves possess unique microbial community structure.• Cavernicoles could be important candidates for antibiotic production.• Cavernicoles are important for biogeochemical cycling.

Microbiome Community Structure and Functional Gene Partitioning in Different Micro-Niches Within a Sporocarp-Forming Fungus

Thelephora ganbajun is a wild edible mushroom highly appreciated throughout China. The microbiomes of some fungal sporocarps have been studied, however, their potential functional roles currently remain uncharacterized. Here, functional gene microarrays (GeoChip 5.0) and amplicon sequencing were employed to define the taxonomic and functional attributes within three micro-niches of T. ganbajun. The diversity and composition of bacterial taxa and their functional genes differed significantly (p < 0.01) among the compartments. Among 31,117 functional genes detected, some were exclusively recorded in one sporocarp compartment: 1,334 genes involved in carbon (mdh) and nitrogen fixation (nifH) in the context; 524 genes influencing carbon (apu) and sulfite reduction (dsrB, dsra) in the hymenophore; and 255 genes involved in sulfur oxidation (soxB and soxC) and polyphosphate degradation (ppx) in the pileipellis. These results shed light on a previously unknown microbiome and functional gene partitioning in sporome compartments of Basidiomycota. This also has great implications for their potential ecological and biogeochemical functions, demonstrating a higher genomic complexity than previously thought.

Oxidation of Cytochrome 605 Is the Rate-Limiting Step when Ferrimicrobium acidiphilum Respires Aerobically on Soluble Iron

Proteins that oxidize extracellular substrates in Gram-positive bacteria are poorly understood. Ferrimicrobium acidiphilum is an actinobacterium that respires aerobically on extracellular ferrous ions at pH 1.5. In situ absorbance measurements were conducted on turbid suspensions of intact Fm. acidiphilum using an integrating cavity absorption meter designed for that purpose. Initial velocity kinetic studies monitored the appearance of product ferric ions in the presence of catalytic quantities of cells. Cell-catalyzed iron oxidation obeyed the Michaelis-Menten equation with Km and Vmax values of 71 μM and 0.29 fmol/min/cell, respectively. Limited-turnover kinetic studies were conducted with higher concentrations of cells to detect and monitor changes in the absorbance properties of cellular redox proteins when the cells were exposed to limited quantities of soluble reduced iron. A single a-type cytochrome with reduced absorbance peaks at 448 and 605 nm was the only redox-active chromophore that was visible as the cells respired aerobically on iron. The reduced cytochrome 605 exhibited mathematical and correlational properties that were consistent with the hypothesis that oxidation of the cytochrome constituted the rate-limiting step in the aerobic respiratory process, with a turnover number of 35 ± 2 s-1 Genomic and proteomic analyses showed that Fm. acidiphilum could and did express only two a-type heme copper terminal oxidases. Cytochrome 605 was associated with the terminal oxidase gene that is located between nucleotides 31,090 and 33,039, inclusive, in the annotated circular genome of this bacterium.IMPORTANCE The identities and functions of proteins involved in aerobic respiration on extracellular ferrous ions at acidic pH are poorly understood in the four phyla of Gram-positive eukaryotes and archaea where such activities occur. In situ absorbance measurements were conducted on Fm. acidiphilum as it respired on extracellular iron using an integrating cavity absorption meter that permitted accurate optical measurements in turbid suspensions of the intact bacterium under physiological conditions. The significance of these measurements is that they permitted a direct spectrophotometric examination of the extents and rates of biological electron transfer events in situ under noninvasive physiological conditions without disrupting the complexity of the live cellular environment. One thing is certain: one way to understand how a protein functions in an intact organism is to actually observe that protein as it functions in the intact organism. This paper provides an example of just such an observation.

Bioleaching of pyritic coal wastes: bioprospecting and efficiency of selected consortia

Pyrite-bearing coal wastes are responsible of the formation of acid mine drainage (AMD), and their management to mitigate environmental impacts is a challenge to the coal mine industry in Europe and worldwide. The European CEReS project sought to develop a generic co-processing strategy to reuse and recycle coal wastes, based on removal of AMD generating potential through bioleaching. Chemolitoautotrophic iron- and sulfur-oxidizing microbial consortia were enriched from a Polish coal waste at 30 °C and 48 °C, but not 42 °C. Pyrite leaching yield, determined from bioleaching tests in 2-L stirred bioreactors, was best with the 48 °C endogenous consortium (80%), then the 42 °C exogenous BRGM-KCC consortium (71%), and finally the 30 °C endogenous consortium (50%). 16S rRNA gene-targeted metagenomics from five surface locations on the dump waste revealed a microbial community adapted to the site context, composed of iron- and/or sulfur-oxidizing genera thriving in low pH and metal rich environments and involved in AMD generation. All together, the results confirmed the predisposition of the pyritic coal waste to bioleaching and the potential of endogenous microorganisms for efficient bioleaching at 48 °C. The good leaching yields open the perspective to optimize further and scale-up the bioleaching process.

Shotgun metagenomic sequencing from Manao-Pee cave, Thailand, reveals insight into the microbial community structure and its metabolic potential

Background

Due to the cave oligotrophic environment, this habitat presents a challenge for microorganisms to colonize and thrive. However, it has been well documented that microorganisms play important roles in cave development. Survival of microbes in this unique habitat likely involves a broad range of adaptive capabilities. Recently, cave microbiomes all over the world are of great scientific interest. However, the majority of investigations focused mostly on small subunit ribosomal RNA (16S rRNA) gene, leaving the ecological role of the microbial community largely unknown. Here, we are particularly interested in exploring the taxonomic composition and metabolic potential of microorganisms in soil from Manao-Pee cave, a subterranean limestone cave in the western part of Thailand, by using high-throughput shotgun metagenomic sequencing.

Results

From taxonomic composition analysis using ribosomal RNA genes (rRNA), the results confirmed that Actinobacteria (51.2%) and Gammaproteobacteria (24.4%) were the dominant bacterial groups in the cave soil community. Metabolic potential analysis, based on six functional modules of the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, revealed that functional genes involved in microbial metabolisms are highly represented in this community (40.6%). To better understand how microbes thrive under unfavorable cave condition, we focused on microbial energy metabolism. The results showed that microbial genes involved in oxidative phosphorylation were the most dominant (28.8%) in Manao-Pee cave, and were followed by methane metabolism (20.5%), carbon fixation (16.0%), nitrogen metabolism (14.7%), and sulfur metabolism (6.3%). In addition, microbial genes involved in xenobiotic biodegradation (26 pathways) and in production of secondary metabolites (27 pathways) were also identified.

Conclusion

In addition to providing information on microbial diversity, we also gained insights into microbial adaptations and survival strategies under cave conditions. Based on rRNA genes, the results revealed that bacteria belonging to the Actinobacteria and Gammaproteobacteria were the most abundant in this community. From metabolic potential analysis, energy and nutrient sources that sustain diverse microbial population in this community might be atmospheric gases (methane, carbon dioxide, nitrogen), inorganic sulfur, and xenobiotic compounds. In addition, the presence of biosynthetic pathways of secondary metabolites suggested that they might play important ecological roles in the cave microbiome.

Electronic supplementary material

The online version of this article (10.1186/s12866-019-1521-8) contains supplementary material, which is available to authorized users.

Draft Genome Sequence of the Gram-Positive Neutrophilic Iron-Precipitating Kineosporia sp. Strain A_224

We report here the draft genome sequence of the neutrophilic iron-precipitating Kineosporia sp. strain A_224. Analysis of the predicted genes may improve our knowledge of its role in ochrous formations in natural and technical water systems. This is the first public genome sequence of a Kineosporia aurantiaca strain.

Sulfur Fertilization Changes the Community Structure of Rice Root-, and Soil- Associated Bacteria

Under paddy field conditions, biological sulfur oxidation occurs in the oxidized surface soil layer and rhizosphere, in which oxygen leaks from the aerenchyma system of rice plants. In the present study, we examined community shifts in sulfur-oxidizing bacteria associated with the oxidized surface soil layer and rice roots under different sulfur fertilization conditions based on the 16S ribosomal RNA (rRNA) gene in order to explore the existence of oligotrophic sulfur-oxidizing bacteria in the paddy rice ecosystem. Rice plants were grown in pots with no fertilization (control) or CaCO3 or CaSO4 fertilization. A principal-coordinates analysis (PCoA) showed that CaSO4 fertilization markedly affected bacterial communities associated with rice roots and soil, whereas no significant differences were observed in plant growth among the fertilizer treatments examined. In rice roots, the relative abundance of Acidobacteria, Alphaproteobacteria, Gammaproteobacteria, and TM7 was significantly higher in CaSO4-fertilized pots than in control pots. Alphaproteobacteria, Bradyrhizobiaceae, and Methylocystaceae members were significantly more abundant in CaSO4-fertilized roots than in control roots. On the other hand, the abundance of Actinobacteria and Proteobacteria was lower in CaSO4-fertilized soil than in control soil. These results indicate that the bacteria associated with rice roots and soil responded to the sulfur amendment, suggesting that more diverse bacteria are involved in sulfur oxidation in the rice paddy ecosystem than previously considered.

Thermophilic and alkaliphilic Actinobacteria: biology and potential applications

Microbes belonging to the phylum Actinobacteria are prolific sources of antibiotics, clinically useful bioactive compounds and industrially important enzymes. The focus of the current review is on the diversity and potential applications of thermophilic and alkaliphilic actinobacteria, which are highly diverse in their taxonomy and morphology with a variety of adaptations for surviving and thriving in hostile environments. The specific metabolic pathways in these actinobacteria are activated for elaborating pharmaceutically, agriculturally, and biotechnologically relevant biomolecules/bioactive compounds, which find multifarious applications.

Metatranscriptomic analysis of a high-sulfide aquatic spring reveals insights into sulfur cycling and unexpected aerobic metabolism

Zodletone spring is a sulfide-rich spring in southwestern Oklahoma characterized by shallow, microoxic, light-exposed spring water overlaying anoxic sediments. Previously, culture-independent 16S rRNA gene based diversity surveys have revealed that Zodletone spring source sediments harbor a highly diverse microbial community, with multiple lineages putatively involved in various sulfur-cycling processes. Here, we conducted a metatranscriptomic survey of microbial populations in Zodletone spring source sediments to characterize the relative prevalence and importance of putative phototrophic, chemolithotrophic, and heterotrophic microorganisms in the sulfur cycle, the identity of lineages actively involved in various sulfur cycling processes, and the interaction between sulfur cycling and other geochemical processes at the spring source. Sediment samples at the spring’s source were taken at three different times within a 24-h period for geochemical analyses and RNA sequencing. In depth mining of datasets for sulfur cycling transcripts revealed major sulfur cycling pathways and taxa involved, including an unexpected potential role of Actinobacteria in sulfide oxidation and thiosulfate transformation. Surprisingly, transcripts coding for the cyanobacterial Photosystem II D1 protein, methane monooxygenase, and terminal cytochrome oxidases were encountered, indicating that genes for oxygen production and aerobic modes of metabolism are actively being transcribed, despite below-detectable levels (<1 µM) of oxygen in source sediment. Results highlight transcripts involved in sulfur, methane, and oxygen cycles, propose that oxygenic photosynthesis could support aerobic methane and sulfide oxidation in anoxic sediments exposed to sunlight, and provide a viewpoint of microbial metabolic lifestyles under conditions similar to those seen during late Archaean and Proterozoic eons.

Making a living while starving in the dark: metagenomic insights into the energy dynamics of a carbonate cave

Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO2-fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO2-fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.

RubisCO-based CO2 fixation and C1 metabolism in the actinobacterium Pseudonocardia dioxanivorans CB1190

Pseudonocardia is an actinobacterial genus of interest due to its potential biotechnological, medical and environmental remediation applications, as well as for the ecologically relevant symbiotic relationships it forms with attine ants. Some Pseudonocardia spp. can grow autotrophically, but the genetic basis of this capability has not previously been reported. In this study, we examined autotrophy in Pseudonocardia dioxanivorans CB1190, which can grow using H2 and CO2, as well as heterotrophically. Genomic and transcriptomic analysis of CB1190 cells grown with H2/bicarbonate implicated the Calvin-Benson-Bassham (CBB) cycle in growth-supporting CO2 fixation, as well as a [NiFe] hydrogenase-encoding gene cluster in H2 oxidation. The CBB cycle genes are evolutionarily most related to actinobacterial homologues, although synteny has not been maintained. Ribulose-1,5-bisphosphate carboxylase activity was confirmed in H2/bicarbonate-grown CB1190 cells and was detected in cells grown with the C1 compounds formate, methanol and carbon monoxide. We also demonstrated the upregulation of CBB cycle genes upon exposure of CB1190 to these C1 substrates, and identified genes putatively involved in generating CO2 from the C1 substrates by using RT-qPCR. Finally, the potential for autotrophic growth of other Pseudonocardia spp. was explored, and the ecological implications of autotrophy in attine ant- and plant root-associated Pseudonocardia discussed.

Biomining: metal recovery from ores with microorganisms

Biomining is an increasingly applied biotechnological procedure for processing of ores in the mining industry (biohydrometallurgy). Nowadays the production of copper from low-grade ores is the most important industrial application and a significant part of world copper production already originates from heap or dump/stockpile bioleaching. Conceptual differences exist between the industrial processes of bioleaching and biooxidation. Bioleaching is a conversion of an insoluble valuable metal into a soluble form by means of microorganisms. In biooxidation, on the other hand, gold is predominantly unlocked from refractory ores in large-scale stirred-tank biooxidation arrangements for further processing steps. In addition to copper and gold production, biomining is also used to produce cobalt, nickel, zinc, and uranium. Up to now, biomining has merely been used as a procedure in the processing of sulfide ores and uranium ore, but laboratory and pilot procedures already exist for the processing of silicate and oxide ores (e.g., laterites), for leaching of processing residues or mine waste dumps (mine tailings), as well as for the extraction of metals from industrial residues and waste (recycling). This chapter estimates the world production of copper, gold, and other metals by means of biomining and chemical leaching (bio-/hydrometallurgy) compared with metal production by pyrometallurgical procedures, and describes new developments in biomining. In addition, an overview is given about metal sulfide oxidizing microorganisms, fundamentals of biomining including bioleaching mechanisms and interface processes, as well as anaerobic bioleaching and bioleaching with heterotrophic microorganisms.

Co-occurrence patterns of plants and soil bacteria in the high-alpine subnival zone track environmental harshness

Plants and soil microorganisms interact to play a central role in ecosystem functioning. To determine the potential importance of biotic interactions in shaping the distributions of these organisms in a high-alpine subnival landscape, we examine co-occurrence patterns between plant species and bulk soil bacteria abundances. In this context, a co-occurrence relationship reflects a combination of several assembly processes: that both parties can disperse to the site, that they can survive the abiotic environmental conditions, and that interactions between the biota either facilitate survival or allow for coexistence. Across the entire landscape, 31% of the bacterial sequences in this dataset were significantly correlated to the abundance distribution of one or more plant species. These sequences fell into 14 clades, 6 of which are related to bacteria that are known to form symbioses with plants in other systems. Abundant plant species were more likely to have significant as well as stronger correlations with bacteria and these patterns were more prevalent in lower altitude sites. Conversely, correlations between plant species abundances and bacterial relative abundances were less frequent in sites near the snowline. Thus, plant-bacteria associations became more common as environmental conditions became less harsh and plants became more abundant. This pattern in co-occurrence strength and frequency across the subnival landscape suggests that plant-bacteria interactions are important for the success of life, both below- and above-ground, in an extreme environment.