Glacial melting in the Tibetan Plateau affects the water resources of millions of people. This study finds that—partly owing to changes in atmospheric circulations and precipitation patterns—the most intensive glacier shrinkage is in the Himalayan region, whereas glacial retreat in the Pamir Plateau region is less apparent.

Different glacier status with atmospheric circulations in Tibetan Plateau and surroundings

Heavy metals in soils

Lithotrophic sulfur oxidation is an ancient metabolic process. Ecologically and taxonomically diverged prokaryotes have differential abilities to utilize different reduced sulfur compounds as lithotrophic substrates. Different phototrophic or chemotrophic species use different enzymes, pathways and mechanisms of electron transport and energy conservation for the oxidation of any given substrate. While the mechanisms of sulfur oxidation in obligately chemolithotrophic bacteria, predominantly belonging to Beta- (e.g. Thiobacillus) and Gammaproteobacteria (e.g. Thiomicrospira), are not well established, the Sox system is the central pathway in the facultative bacteria from Alphaproteobacteria (e.g. Paracoccus). Interestingly, photolithotrophs such as Rhodovulum belonging to Alphaproteobacteria also use the Sox system, whereas those from Chromatiaceae and Chlorobi use a truncated Sox complex alongside reverse-acting sulfate-reducing systems. Certain chemotrophic magnetotactic Alphaproteobacteria allegedly utilize such a combined mechanism. Sulfur-chemolithotrophic metabolism in Archaea, largely restricted to Sulfolobales, is distinct from those in Bacteria. Phylogenetic and biomolecular fossil data suggest that the ubiquity of sox genes could be due to horizontal transfer, and coupled sulfate reduction/sulfide oxidation pathways, originating in planktonic ancestors of Chromatiaceae or Chlorobi, could be ancestral to all sulfur-lithotrophic processes. However, the possibility that chemolithotrophy, originating in deep sea, is the actual ancestral form of sulfur oxidation cannot be ruled out.

Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea.

Evolution of protein molecules. I. Protein synthesis

Next generation sequencing (NGS) technologies have impressively accelerated research in biological science during the last years by enabling the production of large volumes of sequence data to a drastically lower price per base, compared to traditional sequencing methods. The recent and ongoing developments in the field allow addressing research questions in plant-microbe biology that were not conceivable just a few years ago. The present review provides an overview of NGS technologies and their usefulness for the analysis of microorganisms that live in association with plants. Possible limitations of the different sequencing systems, in particular sources of errors and bias, are critically discussed and methods are disclosed that help to overcome these shortcomings. A focus will be on the application of NGS methods in metagenomic studies, including the analysis of microbial communities by amplicon sequencing, which can be considered as a targeted metagenomic approach. Different applications of NGS technologies are exemplified by selected research articles that address the biology of the plant associated microbiota to demonstrate the worth of the new methods.

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Analysis of plant microbe interactions in the era of next generation sequencing technologies.

Nitrogen (N) and/or phosphorus (P) limitation to primary productivity and other biological processes can change in a variety of ways as ecosystems develop. How N limitation and P limitation change from the early to the late stages of a secondary succession following farmland abandonment remains unclear in karst ecosystems in southwest China. We used community foliar N:P ratio, soil alkaline phosphatase activity (APA) and other indicators of nutrient status (soil organic carbon [SOC], total soil N [TN], and total soil P [TP], Alkali-hydrolyzable N [AN], and available soil phosphorus [AP] concentrations) to examine changes in N and P status during secondary vegetation succession. Four types of plant communities (grasslands, shrublands, secondary forest, and primary forest) represented the early, middle, late, and very late successional stages, respectively. Community foliar N:P ratio, APA, and APA per unit SOC increased as succession proceeded from the grassland to the secondary and primary forest communities. Moreover, community foliar N:P ratios in the grassland were positively correlated with soil TN, while community foliar N:P ratios in the secondary forest and primary forest were negatively correlated with soil TP, but were not correlated with soil TN. Community foliar N:P ratios in the shrubland were not correlated with either soil TN or TP. Our results suggest that the grassland in the karst region of southwest China is N limited, that the secondary and primary forests are P limited, and that the shrubland is constrained by N and P together or by other nutrients.

Changes in nitrogen and phosphorus limitation during secondary succession in a karst region in southwest China

Soil erosion rates in two karst peak-cluster depression basins of northwest Guangxi, China: Comparison of the RUSLE model with 137Cs measurements

A novel bacterial species, Rhodocista pekingensis sp. nov., was isolated from a municipal wastewater treatment plant and characterized by polyphasic taxonomy. Cells of R. pekingensis were gram-negative, motile by a single polar flagellum, vibrioid to spiral, 0.6-0.8 microm in width and 0.8-1.5 microm in length. R-bodies were not observed. Phototrophically grown cells contained lamellar photosynthetic membranes and bacteriochlorophyll a. Cell growth was anaerobically phototrophic or aerobically chemoheterotrophic. Anaerobically grown cultures were pink-reddish. Thiamin and vitamin B12, but not biotin, were required for growth and 0.05% yeast extract stimulated growth. Acetate, lactate, pyruvate and succinate supported growth. Cysts were formed when butyrate was used as the sole carbon source. Molecular hydrogen (H2), but not sulfide or thiosulfate, was used as an electron donor. The major cellular quinone was Q-9. The DNA G + C content of cells was 68.8 mol%. The type strain of Rhodocista pekingensis is 3-pT (=AS 1.2194T=JCM 11689T).

Rhodocista pekingensis sp. nov., a cyst-forming phototrophic bacterium from a municipal wastewater treatment plant.

Actinobacteria are known for their metabolic potential of producing diverse secondary metabolites such as antibiotics. Actinobacteria also playimportant roles in biogeochemical cycling and how soils develop. However, little is known about the effect of the vegetation type on the actinobacterial community structures in soils from arid regions. For these reasons, we have analyzed the actinobacterial communities of five types of ecosystem (tree grove, shrub, meadow, desert, and farm) in the Heihe river basin. Using 16S rRNA high-throughput sequencing, we found 11 classes of Actinobacteria, with dominant classes of Actinobacteria (36.2%), Thermoleophilia (28.3%), Acidimicrobiia (19.4%). Five classes, 15 orders, 20 families and 36 genera were present in all samples. The dominant generalist genera were Gaiella, Solirubrobacter, Nocardioides, Mycobacterium, and Pseudonocardia. The actinobacterial community structures were significantly affected by the environment and vegetation type. The diversity of the actinobacterial community in the desert ecosystem was high, and this ecosystem harbored the highest proportion of unclassified sequences, representing rare Actinobacteria. Functional metagenomic prediction, using PICRUSt, indicated that Actinobacteria play an important role in nitrogen cycling in both desert and cultivated farm ecosystems.

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Variation in Actinobacterial Community Composition and Potential Function in Different Soil Ecosystems Belonging to the Arid Heihe River Basin of Northwest China.

There is compelling evidence that glaciers are retreating in many mountainous areas of the world due to global warming. With this glacier retreat, new habitats are being exposed that are colonized by microorganisms whose diversity and function are less well studied. Here, we characterized bacterial diversity along the chronosequences of the glacier No. 1 foreland that follows glacier retreat. An average of 10 000 sequences was obtained from each sample by 454 pyrosequencing. Using non-parametric and rarefaction estimated analysis, we found bacterial phylotype richness was high. The bacterial species turnover rate was especially high between sites exposed for 6 and 10 yr. Pyrosequencing showed tremendous bacterial diversity, among which the Acidobacteria, Actinobacteria, Bacteroidetes and Proteobacteria were found to be present at larger numbers at the study area. Meanwhile, the proportion of Bacteroidetes and Proteobacteria decreased and the proportion of Acidobacteria increased along the chronosequences. Some known functional bacterial genera were also detected and the sulfur- and sulfate-reducing bacteria were present in a lower proportion of sequences. These findings suggest that high-throughput pyrosequencing can comprehensively detect bacteria in the foreland, including rare groups, and give a deeper understanding of the bacterial community structure and variation along the chronosequences.

https://iopscience.iop.org/article/10.1088/1748-9326/7/1/014038/pdf

Wei Zhang

Papers

Changes in nitrogen and phosphorus limitation during secondary succession in a karst region in southwest China

Soil erosion rates in two karst peak-cluster depression basins of northwest Guangxi, China: Comparison of the RUSLE model with 137Cs measurements

Rhodocista pekingensis sp. nov., a cyst-forming phototrophic bacterium from a municipal wastewater treatment plant.

Variation in Actinobacterial Community Composition and Potential Function in Different Soil Ecosystems Belonging to the Arid Heihe River Basin of Northwest China.

Bacterial diversity in the foreland of the Tianshan No. 1 glacier, China