Bacillus alkalidiazotrophicus sp. nov., a diazotrophic, low salt-tolerant alkaliphile isolated from Mongolian soda soil

Chemical Proprieties of Biopolymers (Chitin/Chitosan) and Their Synergic Effects with Endophytic Bacillus Species: Unlimited Applications in Agriculture

Over the past decade, reckless usage of synthetic pesticides and fertilizers in agriculture has made the environment and human health progressively vulnerable. This setting leads to the pursuit of other environmentally friendly interventions. Amongst the suggested solutions, the use of chitin and chitosan came about, whether alone or in combination with endophytic bacterial strains. In the framework of this research, we reported an assortment of studies on the physico-chemical properties and potential applications in the agricultural field of two biopolymers extracted from shrimp shells (chitin and chitosan), in addition to their uses as biofertilizers and biostimulators in combination with bacterial strains of the genus Bacillus sp. (having biochemical and enzymatic properties).

Soil bacterial communities of Sahara and Gibson deserts: Physiological and taxonomical characteristics

The purpose of this research was to investigate the structure of soil bacteria communities present in the Gibson (Australia) and the Sahara (Egypt) deserts, as well as to estimate strain survivability under different environmental factors. It should be noticed that the screening of bacterial resistance to wide spectra of principally different stress conditions was performed for the first time. Experiments were conducted with culturable bacterial communities. Strains were identified using 16S rRNA sequencing, and stress-tolerance was estimated by growing strains in various nutrient media. In order to characterize the community the epifluorescent microscopy and multisubstrate testing were also performed. High bacterial abundance in the desert soils was detected, and there was seen a significant proportion of culturable cells. The close numbers of psychotropic and mesophilic bacteria in arid ecosystems were revealed. The representatives of the Actinobacteria phylum were dominant in the microbial communities, and Firmicutes, Proteobacteria, and Bacteroidetes phyla representatives were also identified. Tolerance of the axenic bacterial cultures, isolated from arid desert ecotopes, to temperature, pH, salts (KCl, NaCl, MgSO4, NaHCO3), strong oxidizers (Mg(ClO4)2), and antibiotics (ampicillin, cephalexin, chloramphenicol, tetracycline, doxycycline, kanamycin, rifampicin) was studied. The bacterial isolates were characterized by polyextremotolerance and by the ability to maintain metabolic activity in vitro while influenced by a wide range of physicochemical and biotic factors.

Anaerobacillus isosaccharinicus sp. nov., an alkaliphilic bacterium which degrades isosaccharinic acid

Strain NB2006^T was isolated from an isosaccharinate-degrading, nitrate-reducing enrichment culture in minimal freshwater medium at pH 10. Analysis of the 16S rRNA gene sequence indicated that this strain was most closely related to species of the newly established genus Anaerobacillus. This was supported by phenotypic and metabolic characterisation that showed that NB2006^T was rod-shaped, Gram-stain-positive, motile and formed endospores. It was an aerotolerant anaerobe and an obligate alkaliphile that grew at pH 8.5-11, could tolerate up to 6 % (w/v) NaCl, and grew at a temperature between 10 and 40 °C. In addition, it could utilise a number of organic substrates, and was able to reduce nitrate and arsenate. The predominant cellular fatty acids were C_16 : 0, C_16 : 1ω11c, anteiso-C_15 : 0, iso-C_15 : 0, C_16 : 1ω7c/iso-C_15 : 0 2-OH and C_14 : 0. The cell wall peptidoglycan contained meso-diaminopimelic acid and the DNA G+C content was 37.7 mol%. In silico DNA-DNA hybridization with the four known species of the genus Anaerobacillus showed 21.8, 21.9, 22.4, and 21.5 % relatedness to Anaerobacillusarseniciselenatis DSM 15340^T, Anaerobacilus alkalidiazotrophicus DSM 22531^T, Anaerobacillusalkalilacustris DSM 18345^T, and Anaerobacillus macyae DSM 16346^T, respectively. NB2006^T differed from strains of other species of the genus Anaerobacillus in its ability to metabolise isosaccharinate, an alkaline hydrolysis product of cellulose. On the basis of the consensus of phylogenetic and phenotypic analyses, this strain represents a novel species of the genus Anaerobacillus, for which the name Anaerobacillus isosaccharinicus sp. nov. is proposed. The type strain is NB2006^T (=DSM 100644^T=LMG 30032^T).

Draft Genome Sequences of Four Alkaliphilic Bacteria Belonging to the Anaerobacillus Genus

The draft genomes of the alkaliphilic, anaerobic bacteria, Anaerobacillus arseniciselenatis, A. alkalidiazotrophicus, and A. alkalilacustris, and a novel closely related isolate of the Anaerobacillus genus are reported here. These assembled genomes will help identify, at the molecular level, the phenotypic differences between the species of this poorly characterized genus.

Three novel bacteriophages isolated from the East African Rift Valley soda lakes

Background

Soda lakes are unique environments in terms of their physical characteristics and the biology they harbour. Although well studied with respect to their microbial composition, their viral compositions have not, and consequently few bacteriophages that infect bacteria from haloalkaline environments have been described.

Methods

Bacteria were isolated from sediment samples of lakes Magadi and Shala. Three phages were isolated on two different Bacillus species and one Paracoccus species using agar overlays. The growth characteristics of each phage in its host was investigated and the genome sequences determined and analysed by comparison with known phages.

Results

Phage Shbh1 belongs to the family Myoviridae while Mgbh1 and Shpa belong to the Siphoviridae family. Tetranucleotide usage frequencies and G + C content suggests that Shbh1 and Mgbh1 do not regularly infect, and have therefore not evolved with, the hosts they were isolated on here. Shbh1 was shown capable of infecting two different Bacillus species from the two different lakes demonstrating its potential broad-host range. Comparative analysis of their genome sequence with known phages revealed that, although novel, Shbh1 does share substantial amino acid similarity with previously described Bacillus infecting phages (Grass, phiNIT1 and phiAGATE) and belongs to the Bastille group, while Mgbh1 and Shpa are highly novel.

Conclusion

The addition of these phages to current databases should help with metagenome/metavirome annotation efforts. We describe a highly novel Paracoccus infecting virus (Shpa) which together with NgoΦ6 and vB_PmaS_IMEP1 is one of only three phages known to infect Paracoccus species but does not show similarity to these phages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12985-016-0656-6) contains supplementary material, which is available to authorized users.

Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond

The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 prokaryotic phyla were detected, and the dominant prokaryotic phyla accounted for more than 95 % of the reads consisting of Planctomycetes, Bacteroidetes, candidate division TM7, Deinococcus-Thermus, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota. Diversity indices indicated that operational taxonomic unit (OTU) richness decreases drastically with increasing salinity in the pond system. A total of 471 OTUs were found at 3.4 % salinity whereas 49 OTUs were detected in pond SP211 (25 % salinity), and only 19 OTUs in the crystallization pond at 32 % salinity (SP230F). Along the salinity gradient, archaeal community gradually replaced bacterial community. Thus, archaeal community accounted for 0.4 % in Lake Abijata while 99.0 % in pond SP230F. This study demonstrates that salinity appears to be the key environmental parameter in structuring the prokaryotic communities of haloalkaline environments. Further, it confirmed that the prokaryotic diversity in Lake Abijata is high and it harbors taxa with low or no phylogenetic similarities to existing prokaryotic taxa and thus represents novel microorganisms.

Genome Sequence of Anaerobacillus macyae JMM-4T (DSM 16346), the First Genomic Information of the Newly Established Genus Anaerobacillus

Anaerobacillus macyae JMM-4^T (DSM 16346) is a Gram-positive, spore-forming, strictly anaerobic, and arsenate-respiring bacterium. Here, we report the 4.26-Mb genome sequence of A. macyae JMM-4^T, which is the first genome information of the newly established genus Anaerobacillus.

Functional microbiology of soda lakes

Soda lakes represent unique permanently haloalkaline system. Despite the harsh conditions, they are inhabited by abundant, mostly prokaryotic, microbial communities. This review summarizes results of studies of main functional groups of the soda lake prokaryotes responsible for carbon, nitrogen and sulfur cycling, including oxygenic and anoxygenic phototrophs, aerobic chemolithotrophs, fermenting and respiring anaerobes. The main conclusion from this work is that the soda lakes are very different from other high-salt systems in respect to microbial richness and activity. The reason for this difference is determined by the major physico-chemical features of two dominant salts - NaCl in neutral saline systems and sodium carbonates in soda lakes, that are influencing the amount of energy required for osmotic adaptation.

Evolution in the Bacillaceae

The family Bacillaceae constitutes a phenotypically diverse and globally ubiquitous assemblage of bacteria. Investigation into how evolution has shaped, and continues to shape, this family has relied on several widely ranging approaches from classical taxonomy, ecological field studies, and evolution in soil microcosms to genomic-scale phylogenetics, laboratory, and directed evolution experiments. One unifying characteristic of the Bacillaceae , the endospore, poses unique challenges to answering questions regarding both the calculation of evolutionary rates and claims of extreme longevity in ancient environmental samples.

Microbial diversity and biogeochemical cycling in soda lakes

Soda lakes contain high concentrations of sodium carbonates resulting in a stable elevated pH, which provide a unique habitat to a rich diversity of haloalkaliphilic bacteria and archaea. Both cultivation-dependent and -independent methods have aided the identification of key processes and genes in the microbially mediated carbon, nitrogen, and sulfur biogeochemical cycles in soda lakes. In order to survive in this extreme environment, haloalkaliphiles have developed various bioenergetic and structural adaptations to maintain pH homeostasis and intracellular osmotic pressure. The cultivation of a handful of strains has led to the isolation of a number of extremozymes, which allow the cell to perform enzymatic reactions at these extreme conditions. These enzymes potentially contribute to biotechnological applications. In addition, microbial species active in the sulfur cycle can be used for sulfur remediation purposes. Future research should combine both innovative culture methods and state-of-the-art 'meta-omic' techniques to gain a comprehensive understanding of the microbes that flourish in these extreme environments and the processes they mediate. Coupling the biogeochemical C, N, and S cycles and identifying where each process takes place on a spatial and temporal scale could unravel the interspecies relationships and thereby reveal more about the ecosystem dynamics of these enigmatic extreme environments.

Microbial degradation of isosaccharinic acid at high pH

Intermediate-level radioactive waste (ILW), which dominates the radioactive waste inventory in the United Kingdom on a volumetric basis, is proposed to be disposed of via a multibarrier deep geological disposal facility (GDF). ILW is a heterogeneous wasteform that contains substantial amounts of cellulosic material encased in concrete. Upon resaturation of the facility with groundwater, alkali conditions will dominate and will lead to the chemical degradation of cellulose, producing a substantial amount of organic co-contaminants, particularly isosaccharinic acid (ISA). ISA can form soluble complexes with radionuclides, thereby mobilising them and posing a potential threat to the surrounding environment or ‘far field'. Alkaliphilic microorganisms sampled from a legacy lime working site, which is an analogue for an ILW-GDF, were able to degrade ISA and couple this degradation to the reduction of electron acceptors that will dominate as the GDF progresses from an aerobic ‘open phase' through nitrate- and Fe(III)-reducing conditions post closure. Furthermore, pyrosequencing analyses showed that bacterial diversity declined as the reduction potential of the electron acceptor decreased and that more specialised organisms dominated under anaerobic conditions. These results imply that the microbial attenuation of ISA and comparable organic complexants, initially present or formed in situ, may play a role in reducing the mobility of radionuclides from an ILW-GDF, facilitating the reduction of undue pessimism in the long-term performance assessment of such facilities.

Are alkalitolerant fungi of the Emericellopsis lineage (Bionectriaceae) of marine origin?

Surveying the fungi of alkaline soils in Siberia, Trans-Baikal regions (Russia), the Aral lake (Kazakhstan), and Eastern Mongolia, we report an abundance of alkalitolerant species representing the Emericellopsis-clade within the Acremonium cluster of fungi (order Hypocreales). On an alkaline medium (pH ca. 10), 34 acremonium-like fungal strains were obtained. One of these was able to develop a sexual morph and was shown to be a new member of the genus Emericellopsis, described here as E. alkalina sp. nov. Previous studies showed two distinct ecological clades within Emericellopsis, one consisting of terrestrial isolates and one predominantly marine. Remarkably, all the isolates from our study sites show high phylogenetic similarity based on six loci (LSU and SSU rDNA, RPB2, TEF1-α, β-tub and ITS region), regardless of their provenance within a broad geographical distribution. They group within the known marine-origin species, a finding that provides a possible link to the evolution of the alkaliphilic trait in the Emericellopsis lineage. We tested the capacities of all newly isolated strains, and the few available reference ex-type cultures, to grow over wide pH ranges. The growth performance varied among the tested isolates, which showed differences in growth rate as well as in pH preference. Whereas every newly isolated strain from soda soils was extremely alkalitolerant and displayed the ability to grow over a wide range of ambient pH (range 4–11.2), reference marine-borne and terrestrial strains showed moderate and no alkalitolerance, respectively. The growth pattern of the alkalitolerant Emericellopsis isolates was unlike that of the recently described and taxonomically unrelated alkaliphilic Sodiomyces alkalinus, obtained from the same type of soils but which showed a narrower preference towards high pH.

Bacillus nanhaiisediminis sp. nov., an alkalitolerant member of Bacillus rRNA group 6

A Gram-stain-positive, rod-shaped bacterium, designated strain NH3T, was isolated from a sediment sample from the South China Sea and was subjected to a polyphasic taxonomic study. The isolate grew optimally at 37 °C and pH 9. Strain NH3T had cell-wall peptidoglycan based on meso-diaminopimelic acid and MK-7 as the predominant menaquinone. The cellular fatty acid profile included significant amounts of iso-C15 : 0 and iso-C14 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The DNA G+C content of strain NH3T was 40.3 mol%. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NH3T was a member of rRNA group 6 of the genus Bacillus, which includes alkalitolerant, alkaliphilic and halotolerant species. The closest phylogenetic relatives were Bacillus akibai 1139T (96.82 % 16S rRNA gene sequence similarity), B. pseudofirmus DSM 8715T (96.76 %), B. okhensis Kh10-101T (96.76 %) and B. alkalidiazotrophicus MS 6T (96.47 %). Strain NH3T could be distinguished from these phylogenetically close neighbours based on a number of phenotypic properties. On the basis of phenotypic and chemotaxonomic characteristics and phylogenetic data, we conclude that strain NH3T ( = CGMCC 1.10116T  = JCM 16507T) merits classification as the type strain of a novel species, for which the name Bacillus nanhaiisediminis sp. nov. is proposed.

Bacillus trypoxylicola sp. nov., xylanase-producing alkaliphilic bacteria isolated from the guts of Japanese horned beetle larvae (Trypoxylus dichotomus septentrionalis)

Three xylanase-producing alkaliphilic strains, SU1T, 36AC4 and 36AC6, were isolated from the guts of larvae of the Japanese horned beetle (Trypoxylus dichotomus septentrionalis). The isolates stained Gram-positive and were aerobic, spore-forming, non-motile and rod-shaped and grew optimally at 30 °C and pH 9. They contained MK-7 as the major isoprenoid quinone and iso-C15 : 0, anteiso-C15 : 0, anteiso-C17 : 0 and iso-C17 : 0 as the major fatty acids. The DNA G+C contents of the strains were 37.4–37.7 mol%. On the basis of 16S rRNA gene sequence similarity, these strains were shown to belong to the genus Bacillus. Although their 16S rRNA gene sequence similarity to the type strains of the alkaliphilic species Bacillus pseudalcaliphilus and B. alcalophilus was 97 %, the novel isolates formed a distinct group in the phylogenetic trees and DNA–DNA relatedness values to the type strains of these species were less than 30 %. Results of physiological and biochemical tests, including salt preference, enabled these strains to be differentiated phenotypically from described Bacillus species. Therefore, strains SU1T, 36AC4 and 36AC6 represent a novel species for which the name Bacillus trypoxylicola sp. nov. is proposed; the type strain is SU1T (=NBRC 102646T =KCTC 13244T).

Natronobacillus azotifigens gen. nov., sp. nov., an anaerobic diazotrophic haloalkaliphile from soda-rich habitats

Gram-positive bacteria capable of nitrogen fixation were obtained in microoxic enrichments from soda soils in south-western Siberia, north-eastern Mongolia, and the Lybian desert (Egypt). The same organisms were obtained in anoxic enrichments with glucose from soda lake sediments in the Kulunda Steppe (Altai, Russia) using nitrogen-free alkaline medium of pH 10. The isolates were represented by thin motile rods forming terminal round endospores. They are strictly fermentative saccharolytic anaerobes but tolerate high oxygen concentrations, probably due to a high catalase activity. All of the strains are obligately alkaliphilic and highly salt-tolerant natronophiles (chloride-independent sodaphiles). Growth was possible within a pH range from 7.5 to 10.6, with an optimum at 9.5-10, and within a salt range from 0.2 to 4 M Na(+), with an optimum at 0.5-1.5 M for the different strains. The nitrogenase activity in the whole cells also had an alkaline pH optimum but was much more sensitive to high salt concentrations compared to the growing cells. The isolates formed a compact genetic group with a high level of DNA similarity. Phylogenetic analysis based on 16S-rRNA gene sequences placed the isolates into Bacillus rRNA group 1 as a separate lineage with Amphibacillus tropicus as the nearest relative. In all isolates the key functional nitrogenase gene nifH was detected. A new genus and species, Natronobacillus azotifigens gen. nov., sp. nov., is proposed to accommodate the novel diazotrophic haloalkaliphiles.