Explore the vast range of titles available.

Acid-tolerant bacteria such as Streptococcus mutans, Acidobacterium capsulatum, Escherichia coli, and Propionibacterium acidipropionici have developed several survival mechanisms to sustain themselves in various acid stress conditions. Some bacteria survive by minor changes in the environmental pH. In contrast, few others adapt different acid tolerance mechanisms, including amino acid decarboxylase acid resistance systems, mainly glutamate-dependent acid resistance (GDAR) and arginine-dependent acid resistance (ADAR) systems. The cellular mechanisms of acid tolerance include cell membrane alteration in Acidithiobacillus thioxidans, proton elimination by F1–F0–ATPase in Streptococcus pyogenes, biofilm formation in Pseudomonas aeruginosa, cytoplasmic urease activity in Streptococcus mutans, synthesis of the protective cloud of ammonia, and protection or repair of macromolecules in Bacillus caldontenax. Apart from cellular mechanisms, there are several acid-tolerant genes such as gadA, gadB, adiA, adiC, cadA, cadB, cadC, speF, and potE that help the bacteria to tolerate the acidic environment. This acid tolerance behavior provides new and broad prospects for different industrial applications and the bioremediation of environmental pollutants. The development of engineered strains with acid-tolerant genes may improve the efficiency of the transgenic bacteria in the treatment of acidic industrial effluents.Key points• Bacteria tolerate the acidic stress by methylating unsaturated phospholipid tail• The activity of decarboxylase systems for acid tolerance depends on pH• Genetic manipulation of acid-tolerant genes improves acid tolerance by the bacteria

Nineteen characterized strains and isolates of acidophilic heterotrophic bacteria were screened for their abilities to catalyse the reductive dissolution of the ferric iron mineral schwertmannite, under oxygen-limiting conditions. Acidocella facilis, Acidobacterium capsulatum, and all of the Acidiphilium, Acidocella and Acidobacterium-like isolates that grew in liquid cultures were able to reduce iron. In contrast, neither Acidisphaera rubrifaciens nor three Acidisphaera-like isolates tested were found to have the capacity for dissimilatory iron reduction. One of two iron-oxidizing Frateuria-like isolates also reduced iron under oxygen-limiting conditions. Microbial dissolution of schwertmannite was paralleled with increased concentrations of soluble ferrous iron and sulfate in microbial cultures, together with increased pH values and decreased redox potentials. While dissimilatory ferric iron reduction has been described previously for Acidiphilium spp., this is this first report of this capacity in Acidocella and the moderate acidophile Acidobacterium. The finding has significant implications for understanding of the biogeochemistry of acidic environments.

Background and aims Altitude, season, and slope aspect have significant impacts on bacterial variation in forest soils. However, it is currently unclear which factor has the greatest influence. Methods Quantitative PCR (qPCR) and high-throughput sequencing were employed to investigate the changes in the bacterial communities with altitude, season and slope aspect in the subtropical forests of Mount Ailao. Results The effects of altitude, season and slope on bacterial abudance were in the order altitude (η 2  = 0.964) > season (η 2  = 0.831) > slope (η 2  = 0.590). In addition, the bacterial abundance increased with altitude, and the rainy season but not the dry season, the eastern slope rather than the western slope had a higher bacterial abundance. Furthermore, altitude (η 2 : 0.877–0.942) and season (η 2 : 0.229–0.761), resulted in higher bacterial α-diversity at low altitudes and in the dry season, respectively. Synergistetes/Verrucomicrobia (low altitude), Acidobacterium (high altitude), Actinobacteria/Planctomycetes (dry season) and Armatipnoadetes (rainy season) were the richest in the soils. Correlation networks showed that bacteria were very stable at higher altitudes and in the dry season. In addition, soil water content, soil organic matter, total nitrogen and ammonium nitrogen were the key edaphic factors significantly affecting the bacterial abundance, α-diversity, and β-diversity. Conclusions Altitudes rather than seasons and slope aspects had the greatest effect on the bacterial communities in subtropical forests. Therefore, we suggest that altitude, season, and slope aspect be considered necessary factors for comprehensive analysis when studying soil microbial changes in different forests. Graphical abstract

We have developed an automatable procedure for reconstructing the tree of life with branch lengths comparable across all three domains. The tree has its basis in a concatenation of 31 orthologs occurring in 191 species with sequenced genomes. It revealed interdomain discrepancies in taxonomic classification. Systematic detection and subsequent exclusion of products of horizontal gene transfer increased phylogenetic resolution, allowing us to confirm accepted relationships and resolve disputed and preliminary classifications. For example, we place the phylum Acidobacteria as a sister group of [delta]-Proteobacteria, support a Gram-positive origin of Bacteria, and suggest a thermophilic last universal common ancestor.

Abstract PurposeThe objective of this study was to investigate the effects of application of biochar and microbial inoculants on the bioavailability of phosphorus and potassium, tomato growth, and the bacterial community in greenhouse soil.Materials and methodsThe experiment was conducted in a greenhouse with tomato mono-cropped for 21 years at Yongqing County of Hebei Province from November 2018 to June 2019. The treatments included conventional fertilization control (CF), 2 t/ha of biochar application (B, manufactured from apricot shell), 75 L/ha of microbial inoculants application (M, containing effective strains of Bacillus megaterium and Paenibacillus mucilaginosus), the mixture of microbial inoculants and biochar application (BM).ResultsThe results showed that the application of 75 L/ha microbial inoculants in greenhouse tomato could increase the yields of tomato by 23.41%, vitamin C (Vc) and soluble sugar concentrations by 14.41% and 13.62%, respectively. The microbial inoculants combined with 2 t/ha biochar enhanced the effects of microbial inoculants on the growth promotion of tomatoes. The application of microbial inoculants combined with biochar increased the P and K accumulation in tomato plants by 28.72–57.14% and 19.53–29.03%, respectively, during the whole growing stage. Moreover, the application of microbial inoculants significantly increased the relative abundance of Bacillus, Paenibacillus, and Flavobacterium and decreased the relative abundance of Acidobacterium.ConclusionsThe application of microbial inoculants improved the bioavailability of phosphorus and potassium and tomato growth by altering the composition of soil bacterial community. These results show the potential of co-application of biochar and microbial inoculants as a potential tool to sustain longer-term production of monoculture vegetable systems in greenhouses.

Only five bacterial phyla with members capable of chlorophyll (Chl)-based phototrophy are presently known. Metagenomic data from the phototrophic microbial mats of alkaline siliceous hot springs in Yellowstone National Park revealed the existence of a distinctive bacteriochlorophyll (BChl)-synthesizing, phototrophic bacterium. A highly enriched culture of this bacterium grew photoheterotrophically, synthesized BChls a and c under oxic conditions, and had chlorosomes and type 1 reaction centers. \"Candidatus Chloracidobacterium thermophilum\" is a BChl-producing member of the poorly characterized phylum ACIDOBACTERIA:

Photochemically induced dynamic nuclear polarization (photo-CIDNP) has been observed in the homodimeric, type-1 photochemical reaction centers (RCs) of the acidobacterium, Chloracidobacterium (Cab.) thermophilum, by 15N magic-angle spinning (MAS) solid-state NMR under continuous white-light illumination. Three light-induced emissive (negative) signals are detected. In the RCs of Cab. thermophilum, three types of (bacterio)chlorophylls have previously been identified: bacteriochlorophyll a (BChl a), chlorophyll a (Chl a), and Zn-bacteriochlorophyll a′ (Zn-BChl a′) (Tsukatani et al. in J Biol Chem 287:5720–5732, 2012). Based upon experimental and quantum chemical 15N NMR data, we assign the observed signals to a Chl a cofactor. We exclude Zn-BChl because of its measured spectroscopic properties. We conclude that Chl a is the primary electron acceptor, which implies that the primary donor is most likely Zn-BChl a′. Chl a and 81-OH Chl a have been shown to be the primary electron acceptors in green sulfur bacteria and heliobacteria, respectively, and thus a Chl a molecule serves this role in all known homodimeric type-1 RCs.

The diversity of bacterial groups of activated sludge samples that received wastewater from four different types of industry was investigated by a nested PCR–DGGE (denaturing gradient gel electrophoresis) approach. Specific 16S rRNA primers were chosen for large bacterial groups (Bacteria and α-Proteobacteria in particular), which dominate activated sludge communities, as well as for actinomycetes, ammonium oxidisers and methanotrophs (types I and II). In addition primers for the new Acidobacterium kingdom were used to observe their community structure in activated sludge. After this first PCR amplification, a second PCR with bacterial primers yielded 16S rRNA gene fragments that were subsequently separated by DGGE, thus generating ‘group-specific DGGE patterns’. The community structure and diversity of the bacterial groups from the different samples was further analysed using different techniques, such as statistical analysis and Shannon diversity index evaluation of the band patterns. By combining the seven DGGE gels, cluster analysis, multidimensional scaling and principal component analysis clearly clustered two of the four activated sludge types separately. It was shown that the combination of molecular and statistical methods can be very useful to differentiate microbial communities.

Formate dehydrogenases (FDHs) are considered particularly useful enzymes in biocatalysis when the regeneration of the cofactor NAD(P)H is required, that is, in chiral synthesis with dehydrogenases. Their utilization is however limited to the recycling of NAD⁺, since all (apart one) of the FDHs characterized so far are strictly specific for this cofactor, and this is a major drawback for their otherwise wide applicability. Despite the many attempts performed to modify cofactor specificity by protein engineering different NAD⁺-dependent FDHs, in the general practice, glucose or phosphite dehydrogenases are chosen for the recycling of NADP⁺. We report on the functional and structural characterization of a new FDH, GraFDH, identified by mining the genome of the extremophile prokaryote Granulicella mallensis MP5ACTX8. The new enzyme displays a valuable stability in the presence of many organic cosolvents as well as double cofactor specificity, with NADP⁺ preferred over NAD⁺ at acidic pH values, at which it also shows the highest stability. The quite low affinities for both cofactors as well as for the substrate formate indicate, however, that the native enzyme requires optimization to be applied as biocatalytic tool. We also determined the crystal structure of GraFDH both as apoprotein and as holoprotein, either in complex with NAD⁺ or NADP⁺. Noticeably, the latter represents the first structure of an FDH enzyme in complex with NADP⁺. This fine picture of the structural determinants involved in cofactor selectivity will possibly boost protein engineering of the new enzyme or other homolog FDHs in view of their biocatalytic exploitation for NADP⁺ recycling.

Here, we report on the construction of a metagenomic library from a chitin-amended disease-suppressive agricultural soil and its screening for genes that encode novel chitinolytic enzymes. The library, constructed in fosmids in an Escherichia coli host, comprised 145,000 clones containing inserts of sizes of 21 to 40 kb, yielding a total of approximately 5.8 GB of cloned soil DNA. Using genetic screenings by repeated PCR cycles aimed to detect gene sequences of the bacterial chitinase A-class (hereby named chi A genes), we identified and characterized five fosmids carrying candidate genes for chitinolytic enzymes. The analysis thus allowed access to the genomic (fosmid-borne) context of these genes. Using the chiA-targeted PCR, which is based on degenerate primers, the five fosmids all produced amplicons, of which the sequences were related to predicted chitinolytic enzyme-encoding genes of four different host organisms, including Stenotrophomonas maltophilia. Sequencing and de novo annotation of the fosmid inserts confirmed that each one of these carried one or more open reading frames that were predicted to encode enzymes active on chitin, including one for a chitin deacetylase. Moreover, the genetic contexts in which the putative chitinolytic enzyme-encoding genes were located were unique per fosmid. Specifically, inserts from organisms related to Burkholderia sp., Acidobacterium sp., Aeromonas veronii, and the chloroflexi Nitrolancetus hollandicus and/or Ktedonobacter racemifer were obtained. Remarkably, the S. maltophilia chiA-like gene was found to occur in two different genetic contexts (related to N. hollandicus/K. racemifer), indicating the historical occurrence of genetic reshufflings in this part of the soil microbiota. One fosmid containing the insert composed of DNA from the N. hollandicus-like organism (denoted 53D1) was selected for further work. Using subcloning procedures, its putative gene for a chitinolytic enzyme was successfully brought to expression in an E. coli host. On the basis of purified protein preparations, the produced protein was characterized as a chitobiosidase of 43.6 kDa, with a pI of 4.83. Given its activity spectrum, it can be typified as a halotolerant chitobiosidase.