Prokaryotic life in a potash-polluted marsh with emphasis on N-metabolizing microorganisms

Diversity of Microorganisms in Biocrusts Surrounding Highly Saline Potash Tailing Piles in Germany

Potash tailing piles located in Germany represent extremely hypersaline locations that negatively affect neighbouring environments and limit the development of higher vegetation. However, biocrusts, as cryptogamic covers, inhabit some of these areas and provide essential ecological functions, but, nevertheless, they remain poorly described. Here, we applied high-throughput sequencing (HTS) and targeted four groups of microorganisms: bacteria, cyanobacteria, fungi and other eukaryotes. The sequencing of the 16S rRNA gene revealed the dominance of Proteobacteria, Cyanobacteria and Actinobacteria. Additionally, we applied yanobacteria-specific primers for a detailed assessment of the cyanobacterial community, which was dominated by members of the filamentous orders Synechococcales and Oscillatoriales. Furthermore, the majority of reads in the studied biocrusts obtained by sequencing of the 18S rRNA gene belonged to eukaryotic microalgae. In addition, sequencing of the internal rDNA transcribed spacer region (ITS) showed the dominance of Ascomycota within the fungal community. Overall, these molecular data provided the first detailed overview of microorganisms associated with biocrusts inhabiting highly saline potash tailing piles and showed the dissimilarities in microbial diversity among the samples.

Uncovering Unique Green Algae and Cyanobacteria Isolated from Biocrusts in Highly Saline Potash Tailing Pile Habitats, Using an Integrative Approach

Potash tailing piles caused by fertilizer production shape their surroundings because of the associated salt impact. A previous study in these environments addressed the functional community "biocrust" comprising various micro- and macro-organisms inhabiting the soil surface. In that previous study, biocrust microalgae and cyanobacteria were isolated and morphologically identified amongst an ecological discussion. However, morphological species identification maybe is difficult because of phenotypic plasticity, which might lead to misidentifications. The present study revisited the earlier species list using an integrative approach, including molecular methods. Seventy-six strains were sequenced using the markers small subunit (SSU) rRNA gene and internal transcribed spacer (ITS). Phylogenetic analyses confirmed some morphologically identified species. However, several other strains could only be identified at the genus level. This indicates a high proportion of possibly unknown taxa, underlined by the low congruence of the previous morphological identifications to our results. In general, the integrative approach resulted in more precise species identifications and should be considered as an extension of the previous morphological species list. The majority of taxa found were common in saline habitats, whereas some were more likely to occur in nonsaline environments. Consequently, biocrusts in saline environments of potash tailing piles contain unique microalgae and cyanobacteria that will possibly reveal several new taxa in more detailed future studies and, hence, provide new data on the biodiversity, as well as new candidates for applied research.

Microbial community structure of relict niter-beds previously used for saltpeter production

From the 16th to the 18th centuries in Japan, saltpeter was produced using a biological niter-bed process and was formed under the floor of gassho-style houses in the historic villages of Shirakawa-go and Gokayama, which are classified as United Nations Educational, Scientific and Cultural Organization (UNESCO) World Heritage Sites. The relict niter-beds are now conserved in the underfloor space of gassho-style houses, where they are isolated from destabilizing environmental factors and retain the ability to produce nitrate. However, little is known about the nitrifying microbes in such relict niter-bed ecosystems. In this study, the microbial community structures within nine relict niter-bed soils were investigated using 454 pyrotag analysis targeting the 16S rRNA gene and the bacterial and archaeal ammonia monooxygenase gene (amoA). The 16S rRNA gene pyrotag analysis showed that members of the phyla Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Planctomycetes were major microbial constituents, and principal coordinate analysis showed that the NO₃⁻, Cl⁻, K⁺, and Na⁺ contents were potential determinants of the structures of entire microbial communities in relict niter-bed soils. The bacterial and archaeal amoA libraries indicated that members of the Nitrosospira-type ammonia-oxidizing bacteria (AOB) and “Ca. Nitrososphaera”-type ammonia-oxidizing archaea (AOA), respectively, predominated in relict niter-bed soils. In addition, soil pH and organic carbon content were important factors for the ecological niche of AOB and AOA in relict niter-bed soil ecosystems.

Survival of the fittest: overcoming oxidative stress at the extremes of Acid, heat and metal

The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores catalyze oxidative reactions attacking microbial cell surfaces including lipids, proteins and glycosyl groups. Sulfuric acid also promotes hydrocarbon dehydration contributing to the formation of black “burnt” carbon. Oxidative reactions leading to abstraction of electrons is further impacted by heat through an increase in the proportion of reactant molecules with sufficient energy to react. Collectively these factors and particularly those related to metals must be overcome by thermoacidophilic lithoautotrophs in order for them to survive and proliferate. The necessary mechanisms to achieve this goal are largely unknown however mechanistics insights have been gained through genomic studies. This review focuses on the specific role of metals in this extreme environment with an emphasis on resistance mechanisms in Archaea.

Nitrogen fixation and hydrogen metabolism in cyanobacteria

This review summarizes recent aspects of (di)nitrogen fixation and (di)hydrogen metabolism, with emphasis on cyanobacteria. These organisms possess several types of the enzyme complexes catalyzing N(2) fixation and/or H(2) formation or oxidation, namely, two Mo nitrogenases, a V nitrogenase, and two hydrogenases. The two cyanobacterial Ni hydrogenases are differentiated as either uptake or bidirectional hydrogenases. The different forms of both the nitrogenases and hydrogenases are encoded by different sets of genes, and their organization on the chromosome can vary from one cyanobacterium to another. Factors regulating the expression of these genes are emerging from recent studies. New ideas on the potential physiological and ecological roles of nitrogenases and hydrogenases are presented. There is a renewed interest in exploiting cyanobacteria in solar energy conversion programs to generate H(2) as a source of combustible energy. To enhance the rates of H(2) production, the emphasis perhaps needs not to be on more efficient hydrogenases and nitrogenases or on the transfer of foreign enzymes into cyanobacteria. A likely better strategy is to exploit the use of radiant solar energy by the photosynthetic electron transport system to enhance the rates of H(2) formation and so improve the chances of utilizing cyanobacteria as a source for the generation of clean energy.

Archaeal diversity at the great salt plains of Oklahoma described by cultivation and molecular analyses

The Great Salt Plains of Oklahoma is a natural inland terrestrial hypersaline environment that forms evaporite crusts of mainly NaCl. Previous work described the bacterial community through the characterization of 105 isolates from 46 phylotypes. The current report describes the archaeal community through both microbial isolation and culture-independent techniques. Nineteen distinct archaea were isolated, and ten were characterized phenetically. Included were isolates phylogenetically related to Haloarcula, Haloferax, Halorubrum, Haloterrigena, and Natrinema. The isolates were aerobic, non-motile, Gram-negative organisms and exhibited little capacity for fermentation. All of the isolates were halophilic, with most requiring at least 15% salinity for growth, and all grew at 30% salinity. The isolates were mainly mesothermic and could grow at alkaline pH (8.5). A 16S rRNA gene library was generated by polymerase chain reaction amplification of direct soil DNA extracts, and 200 clones were sequenced and analyzed. At 99% and 94% sequence identity, 36 and 19 operational taxonomic units (OTUs) were detected, respectively, while 53 and 22 OTUs were estimated by Chao1, respectively. Coverage was relatively high (100% and 59% at 89% and 99% sequence identity, respectively), and the Shannon Index was 3.01 at 99% sequence identity, comparable to or somewhat lower than hypersaline habitats previously studied. Only sequences from Euryarchaeota in the Halobacteriales were detected, and the strength of matches to known sequences was generally low, most near 90% sequence identity. Large clusters were observed that are related to Haloarcula and Halorubrum. More than two-thirds of the sequences were in clusters that did not have close relatives reported in public databases.

Bacterial associates of arboreal ants and their putative functions in an obligate ant-plant mutualism

Bacterial communities are highly diverse and have great ecological importance. In the present study, we used an in silico analysis of terminal restriction fragments (tRF) to characterize the bacterial community of the plant ant Pseudomyrmex ferrugineus. This species is an obligate inhabitant of Acacia myrmecophytes and feeds exclusively on plant-derived food sources. Ants are the dominant insect group in tropical rain forests. Associations of ants with microbes, which contribute particularly to the ants' nitrogen nutrition, could allow these insects to live on mostly or entirely plant-based diets and could thus contribute to the explanation of the high abundances that are reached by tropical ants. We found tRF patterns representing at least 30 prokaryotic taxa, of which the Acidobacteria, Actinobacteria, Bacteroidetes, Firmicutes, Planctomycetes, Proteobacteria, and Spirochaetes comprised 93%. Because most bacterial taxa were found in all ant-derived samples studied and because the bacteria detected on the ants' host plant revealed little overlap with this community, we regard our results as reliably representing the bacterial community that is associated with P. ferrugineus. Genera with a likely function as ant symbionts were Burkholderia, Pantoea, Weissella, and several members of the Enterobacteriaceae. The presence of these and various other groups was confirmed via independent PCR and cultivation approaches. Many of the bacteria that we detected belong to purportedly N-fixing taxa. Bacteria may represent important further partners in ant-plant mutualisms, and their influences on ant nutrition can contribute to the extraordinary abundance and evolutionary success of tropical arboreal ants.

Biodiversity of arbuscular mycorrhizal fungi in roots and soils of two salt marshes

The occurrence of arbuscular mycorrhizal fungi (AMF) was assessed by both morphological and molecular criteria in two salt marshes: (i) a NaCl site of the island Terschelling, Atlantic Coast, the Netherlands and (ii) a K(2)CO(3) marsh at Schreyahn, Northern Germany. The overall biodiversity of AMF, based on sequence analysis, was comparably low in roots at both sites. However, the morphological spore analyses from soil samples of both sites exhibited a higher AMF biodiversity. Glomus geosporum was the only fungus of the Glomerales that was detected both as spores in soil samples and in roots of the AMF-colonized salt plants Aster tripolium and Puccinellia sp. at both saline sites and on all sampling dates (one exception). In roots, sequences of Glomus intraradices prevailed, but this fungus could not be identified unambiguously from DNA of soil spores. Likewise, Glomus sp. uncultured, only deposited as sequence in the database, was widely detected by DNA sequencing in root samples. All attempts to obtain the corresponding sequences from spores isolated from soil samples failed consistently. A small sized Archaeospora sp. was detected, either/or by morphological and molecular analyses, in roots or soil spores, in dead AMF spores or orobatid mites. The study noted inconsistencies between morphological characterization and identification by DNA sequencing of the 5.8S rDNA-ITS2 region or part of the 18S rDNA gene. The distribution of AMF unlikely followed the salt gradient at both sites, in contrast to the zone formation of plant species. Zygotes of the alga Vaucheria erythrospora (Xanthophyceae) were retrieved and should not be misidentified with AMF spores.