Dynamic succession of chickpea rhizobia over years and sampling sites in Xinjiang,China

Aims

Cyanobacterial and algal communities have a large effect on biocrust formation and development. Biocrust species and abundance vary spatially and temporally due to different environmental factors. The relationships among cyanobacterial and algal communities, and biocrust function have been studied extensively. Lacking, however, are studies of temporal changes in a similar landscape where environmental conditions are similar, but where biocrust formation is different.

Methods

Biocrusts of different ages were located in the Loess Plateau in an area that had experienced a landslide. We examined changes in cyanobacterial and algal communities, carbon, nutrients, and the composition of dissolved organic matter in the topsoil, and the relationships among the community and soil characteristics using redundancy analysis.

Results

Phormidium tenue (Cyanophyta) dominated in all biocrusts, and co-dominated in a newly formed crust with Euglena sp. (Euglenophyta). Oscillatoria sp. (Cyanophyta) increased with biocrust age. Oscillatoria was positively correlated with carbon fixation and nutrient (nitrogen and phosphorus) accumulation in topsoils.

Conclusions

While incubation of Phormidium tenue and Euglena sp. is suggested for rapid biocrust formation at an early stage, increasing the abundance of Phormidium tenue and Oscillatoria sp. can promote carbon fixation and nutrient (nitrogen and phosphorus) accumulation, thereby accelerating biocrusts into a later stage.

     

Biocrusts enhance soil fertility and <Emphasis Type="Italic">Bromus tectorum</Emphasis> growth,and interact with warming to influence germination

Background and aims

Biocrusts are communities of cyanobacteria, mosses, and/or lichens found in drylands worldwide. Biocrusts are proposed to enhance soil fertility and productivity, but simultaneously act as a barrier to the invasive grass, Bromus tectorum, in western North America. Both biocrusts and B. tectorum are sensitive to climate change drivers, yet how their responses might interact to affect dryland ecosystems is unclear.

Methods

Using mesocosms with bare soil versus biocrust cover, we germinated B. tectorum seeds collected from warmed, warmed + watered, and ambient temperature plots within a long-term climate change experiment on the Colorado Plateau, USA. We characterized biocrust influences on soil fertility and grass germination, morphology, and chemistry.

Results

Biocrusts increased soil fertility and B. tectorum biomass, specific leaf area (SLA), and root:shoot ratios. Germination rates were unaffected by mesocosm cover-type. Biocrusts delayed germination timing while also interacting with the warmed treatment to advance, and with the warmed + watered treatment to delay germination.

Conclusions

Biocrusts promoted B. tectorum growth, likely through positive influence on soil fertility which was elevated in biocrust mesocosms, and interacted with seed treatment-provenance to affect germination. Understanding how anticipated losses of biocrusts will affect invasion dynamics will require further investigation of how plant plasticity/adaptation to specific climate drivers interact with soil and biocrust properties.

     

Trade-off between C and N recycling and N<Subscript>2</Subscript>O emissions of soils with summer cover crops in subtropical agrosystems

Aims

Biological soil crusts (biocrusts) are soil-surface communities in drylands, dominated by cyanobacteria, mosses, and lichens. They provide key ecosystem functions by increasing soil stability and influencing soil hydrologic, nutrient, and carbon cycles. Because of this, methods to reestablish biocrusts in damaged drylands are needed. Here we test the reintroduction of field-collected vs. greenhouse-cultured biocrusts for rehabilitation.

Methods

We collected biocrusts for 1) direct reapplication, and 2) artificial cultivation under varying hydration regimes. We added field-collected and cultivated biocrusts (with and without hardening treatments) to bare field plots and monitored establishment.

Results

Both field-collected and cultivated cyanobacteria increased cover dramatically during the experimental period. Cultivated biocrusts established more rapidly than field-collected biocrusts, attaining ~82% cover in only one year, but addition of field-collected biocrusts led to higher species richness, biomass (as assessed by chlorophyll a) and level of development. Mosses and lichens did not establish well in either case, but late successional cover was affected by hardening and culture conditions.

Conclusions

This study provides further evidence that it is possible to culture biocrust components from later successional materials and reestablish cultured organisms in the field. However, more research is needed into effective reclamation techniques.

     

Carbon mineralization and microbial activity in agricultural topsoil and subsoil as regulated by root nitrogen and recalcitrant carbon concentrations

Background and aims

Biocrust morphology is often used to infer ecological function, but morphologies vary widely in pigmentation and thickness. Little is known about the links between biocrust morphology and the composition of constituent microbial community. This study aimed to examine these links using dryland crusts varying in stage and morphology.

Methods

We compared the microbial composition of three biocrust developmental stages (Early, Mid, Late) with bare soil (Bare) using high Miseq Illumina sequencing. We used standard diversity measures and network analysis to explore how microbe-microbe associations changed with biocrust stage.

Results

Biocrust richness and diversity increased with increasing stage, and there were marked differences in the microbial signatures among stages. Bare and Late stages were dominated by Alphaproteobacteria, but Cyanobacteria was the dominant phylum in Early and Mid stages. The greatest differences in microbial taxa were between Bare and Late stages. Network analysis indicated highly-connected hubs indicative of small networks.

Conclusions

Our results indicate that readily discernible biocrust features may be good indicators of microbial composition and structure. These findings are important for land managers seeking to use biocrusts as indicators of ecosystem health and function. Treating biocrusts as a single unit without considering crust stage is likely to provide misleading information on their functional roles.

     

Potential for synergy in soil inoculation for nature restoration by mixing inocula from different successional stages

Background and aims

Due to the well-known importance of biocrusts for several ecosystem properties linked to soil functionality, we aim to go deeper into the physiological performance of biocrusts components. Possible functional convergences in the physiology of biocrust constituents would facilitate the understanding of both species and genus distributional patterns and improve the possibility of modelling their response to climate change.

Methods

We measured gas exchange in the laboratory under controlled conditions of lichen- and moss-dominated biocrusts from four environmentally different locations in Europe. Field data were used to determine the natural hydration sources that drive metabolic activity of biocrusts.

Results

Our results show different activity drivers at the four sites. Within site analyses showed similar C fixation for the different crust types in the three sites without hydric stress whilst light use related parameters and respiration at 15 °C were similar in the between sites analyses. There were significant differences in water relations between the biocrusts types, with moss-dominated crusts showing higher maximum and optimum water contents.

Conclusions

The functional type approach for biocrusts can be justified from a physiological perspective when similar values are found in the within and between site analyses, the latter indicating habitat independent adaptation patterns. Our multi-site analyses for biocrusts functional performance provide comparisons of C fluxes and water relations in the plant-soil interface that will help to understand the adaptation ability of these communities to possible environmental changes.

     

Crop mixtures: does niche complementarity hold for belowground resources? An experimental test using rice genotypic pairs

Aims

A growing body of research supports the feasibility of biocrust rehabilitation. Identifying populations of key species that are amenable to cultivation and that are resilient in rehabilitation contexts would advance the efficacy of these technologies. Here we investigate the growth and stress response of the cosmopolitan biocrust moss, Syntrichia ruralis.

Methods

We sampled populations of S. ruralis along a precipitation seasonality gradient from the Colorado Plateau ecoregion of the western United States. We cultivated these populations in an experiment manipulating duration of hydration periods on a weekly cycle. We then treated greenhouse grown materials with brief, stressful watering events, measuring how many events they could survive.

Results

All populations grew at an accelerated rate compared to growth in a natural setting, at least doubling biomass in five months. Increasing duration of hydration periods led to more growth in all but one population. Volunteer biocrust algae and cyanobacteria developed during cultivation, and differed among populations. Greenhouse grown mosses differed in their response to stressful watering, with the most susceptible populations dying at half the number events compared to the most tolerant.

Conclusions

These findings argue for informed selection and deployment of Syntrichia ruralis populations for soil rehabilitation.

     

Development of a novel engineered antibody targeting <Emphasis Type="Italic">Neisseria</Emphasis> species

Objectives

A Neissaria bacterial pilus sugar, bacillosamine, was synthesized and, for the first time, used as a probe to screen a single-chain variable fragment (scFv).

Results

Four Neisseria, Neisseria gonorrhoeae, Neisseria meningitidis, Neisseria sicca and Neisseria subflava, and two negative controls, Streptococcus pneumoniae and Escherichia coli, were tested through ELISA, immunostaining and gold nanoparticle immunological assay. All results indicated that the selected scFv is feasible for the specific detection of Neisseria species via the recognition of bacillosamine.

Conclusions

The recombinant scFv could detect Neisseria strains at 10⁶ CFU/ml.

     

Interactions between soil properties,soil microbes and plants in remnant-grassland and old-field areas: a reciprocal transplant approach

Background and Aims

Biological soil crusts cover about one third of the terrestrial soil surfaces in drylands, fulfilling highly important ecosystem services. Their relevance to global carbon cycling, however, is still under debate.

Methods

We utilized CO₂ gas exchange measurements to investigate the net photosynthetic response of combined cyanobacteria/cyanolichen-, chlorolichen- and moss-dominated biocrusts and their isolated photoautotrophic components to light, temperature, and water. The results were compared with field studies to evaluate their compatibility.

Results

Different biocrust types responded similarly, being inhibited by limited and excess water, saturated by increasing light intensities, and having optimum temperatures. Cyanobacteria/cyanolichen-dominated biocrusts reached their water optimum at lowest contents (0.52–0.78 mm H₂O), were saturated at highest light intensities, and had a comparably high temperature optimum at 37 °C. Chlorolichen-dominated crusts had a medium water optimum (0.75–1.15 mm H₂O), medium saturating light intensities and a moderate temperature optimum of 22 °C. Moss-dominated biocrusts had the highest water optimum (1.76–2.38 mm H₂O), lowest saturating light intensities, and a similar temperature optimum at 22 °C. Isolated photoautotrophs responded similar to complete crusts, only isolated moss stems revealed much lower respiration rates compared to complete crusts.

Conclusions

In addition to their overall functional similarities, cyanobacteria/cyanolichen-dominated biocrusts appeared to be best adapted to predicted climate change of increasing temperatures and smaller precipitation events, followed by chlorolichen-dominated biocrusts. Moss-dominated biocrusts needed by far the largest amounts of water, thus likely being prone to anticipated climate change.

     

Synergistic and antagonistic effects of mixing monospecific soils on plant-soil feedbacks

Background and aims

Disturbance affects the ability of organisms to persist on a site, and disturbance history acts as a filter of community composition. This is true for vascular plants and morphological groups of biocrusts, which respond differently to disturbance. Although functioning arid ecosystems include both groups, filtering of morphological groups of biocrusts has not previously been compared simultaneously with the responses of vascular plants.

Methods

Using a chronosequence approach, cover of vascular plants and biocrusts was examined across chronic disturbance gradients related to invasion by exotic species and grazing by livestock, following the acute disturbance of fire using paired burned and unburned plots in Wyoming big sagebrush on 99 plots.

Results

Cover of vascular plants and biocrusts was related to disturbance more so than abiotic factors of precipitation following fire, soil chemistry, percent coarse fragment and heat load index. Over time since fire of 12–23 years, we saw recovery of early successional groups: short mosses, shallow-rooted perennial grasses and annual forbs. Cover of deep and shallow-rooted perennial grasses and annual forbs increased in cover with intermediate levels of disturbance. Perennial forbs lacked a clear relationship with disturbance. Biocrusts decreased in cover with less disturbance when compared with perennial herbaceous plants but differed in sensitivities. Tall mosses were less sensitive to disturbance compared with lichens. Short mosses increased with some disturbance.

Conclusions

Morphological groups of biocrusts and vascular plants are eliminated with increasing variability in the size of gaps between perennials represented by the standard deviation of gaps between perennials. The inclusion of both groups in assessments of ecosystem recovery following disturbance addresses the fact that recovery of either group does not happen in isolation from the other but with interacting contributions to ecosystem functions.

     

Effects of <Emphasis Type="Italic">Penicillium bilaii</Emphasis> on maize growth are mediated by available phosphorus

Background and aims

Functional traits are promising indicators of global changes and ecosystem processes. Trait responses to environmental conditions have been examined widely in vascular plants. In contrast, few studies have focused on soil lichens and mosses composing biocrusts. We aimed to evaluate the potential of biocrust tissue traits as indicators of changes in climate and soil properties.

Methods

Isotope ratios and nutrient content in biocrust tissue were analyzed in 13 Mediterranean shrublands along an aridity gradient. Differences in tissue traits between biocrust groups (lichens and mosses), and relationships between tissue traits and climatic and soil variables were examined.

Results

Lichens and mosses differed in δ¹³C, δ¹⁵N and N content, indicating distinct physical and physiological attributes. Tissue traits correlated strongly with numerous climatic variables, likely due to a modulator effect on biocrust water relations and metabolism. We found contrasting responses of lichen and moss traits to climate, although they responded similarly to soil properties. Overall, the most responsive trait was δ¹⁵N, suggesting this trait is the best to reflect integrated processes occurring in the atmosphere and soil.

Conclusions

Biocrust tissue traits arise as cost-effective, integrative ecological indicators of global change drivers in Mediterranean ecosystems, with potential applications in response-effect trait frameworks.

     

Expression,purification and characterization of a thermostable leucine dehydrogenase from the halophilic thermophile <Emphasis Type="Italic">Laceyella sacchari</Emphasis>

Objective

A potential thermotolerant l-leucine dehydrogenase from Laceyella sacchari (Ls-LeuDH) was over-expressed in E. coli, purified and characterized.

Results

Ls-LeuDH had excellent thermostability with a specific activity of 183 U/mg at pH 10.5 and 25 °C. It retained a high activity in 200 mM carbonate buffer from pH 9.5 to 11. The optimal temperature for Ls-LeuDH was 60 °C.

Conclusion

It is the first time that a thermostable and highly active LeuDH originating from L. sacchari has been characterized. It may be useful for medical and pharmaceutical applications.

     

Production of caffeoylmalic acid from glucose in engineered <Emphasis Type="Italic">Escherichia coli</Emphasis>

Objectives

To achieve biosynthesis of caffeoylmalic acid from glucose in engineered Escherichia coli.

Results

We constructed the biosynthetic pathway of caffeoylmalic acid in E. coli by co-expression of heterologous genes RgTAL, HpaBC, At4CL2 and HCT2. To enhance the production of caffeoylmalic acid, we optimized the tyrosine metabolic pathway of E. coli to increase the supply of the substrate caffeic acid. Consequently, an E. coli–E. coli co-culture system was used for the efficient production of caffeoylmalic acid. The final titer of caffeoylmalic acid reached 570.1 mg/L.

Conclusions

Microbial production of caffeoylmalic acid using glucose has application potential. In addition, microbial co-culture is an efficient tool for producing caffeic acid esters.

     

Ammonium inhibition through the decoupling of acidification process and methanogenesis in anaerobic digester revealed by high throughput sequencing

Objective

To reveal the shifts of microbial communities along ammonium gradients, and the relationship between microbial community composition and the anaerobic digestion performance using a high throughput sequencing technique.

Results

Methane production declined with increasing ammonium concentration, and was inhibited above 4 g l^?1. The volatile fatty acids, especially acetate, accumulated with elevated ammonium. Prokaryotic populations showed different responses to the ammonium concentration: Clostridium, Tepidimicrobium, Sporanaerobacter, Peptostreptococcus, Sarcina and Peptoniphilus showed good tolerance to ammonium ions. However, Syntrophomonas with poor tolerance to ammonium may be inhibited during anaerobic digestion. During methanogenesis, Methanosarcina was the dominant methanogen.

Conclusion

Excessive ammonium inhibited methane production probably by decoupling the linkage between acidification process and methanogenesis, and finally resulted in different performance in anaerobic digestion.

     

Revegetation modifies patterns of temporal soil respiration responses to extreme-drying-and-rewetting in a semiarid ecosystem

Aims

The artificial cultivation of biocrusts may represent a new low-cost and highly efficient solution to erosion control. However, establishment under varying field environmental conditions is understudied. We tested a variety of methods, arriving at a set of technical recommendations for rapid establishment of moss biocrusts on disturbed slopes, and the industrialization of this process.

Methods

In multiple field experiments, aimed at moss biocrust cultivation and establishment, we considered the following factors: nutrient solutions (control and weekly addition); water-retaining agent (control and addition); plant growth regulator (control and biweekly addition); shading (0, 50%, 70% and 90%); dispersal method (broadcast and spray application). In all cases, we initially inoculated soils with 700 g/m² of moss biocrust materials. We monitored dynamic changes of the coverage and density of moss biocrusts during the cultivation period, and their biomass at the end.

Results

We successfully cultured moss biocrusts in a field setting in as little as two months. Specifically, we found:(1) Regardless of the dispersal method, the nutrient solutions and some degree of shading both increased the coverage, plant density and biomass of moss biocrusts, whereas the water-retaining agent and plant growth regulator had little influence on these parameters. The shading treatments improved the survival rates of moss biocrusts, with the shade rating of 70% exhibiting the best performance. Further, the nutrient solutions had a more positive effect under shaded conditions. (2) The growth of mosses dispersed in the fall exceeded that of mosses dispersed in the summer. (3) Under both dispersal techniques, the maximal coverage of the moss biocrusts exceeded 90%, and the maximal plant density of moss biocrusts reached 120 stems/cm²under broadcast dispersal, and 150 stems/cm², under spray dispersal.

Conclusions

The rapid restoration of moss biocrusts can best be achieved by spray-dispersal or broadcast-dispersal, while also applying Hoagland solution to supply nutrients and maintaining soil moisture at 15–25%. Fall inoculation appears more likely to lead to better moss establishment, in fact, high moss mortality occurred in summer unless shading was used. We have some evidence, observational in fall, and experimental in summer, that moderate shading favors establishment. This technique could feasibly be up scaled and adopted to restore some ecological functions on various types of engineered disturbed surfaces. Over a longer period, the survivorship, succession and sustainability of artificial moss biocrusts should be explored specifically.

     

Does centrifugation matter? Centrifugal force and spinning time alter the plasma metabolome

Background

Centrifugation is an indispensable procedure for plasma sample preparation, but applied conditions can vary between labs.

Aim

Determine whether routinely used plasma centrifugation protocols (1500×g 10 min; 3000×g 5 min) influence non-targeted metabolomic analyses.

Methods

Nuclear magnetic resonance spectroscopy (NMR) and High Resolution Mass Spectrometry (HRMS) data were evaluated with sparse partial least squares discriminant analyses and compared with cell count measurements.

Results

Besides significant differences in platelet count, we identified substantial alterations in NMR and HRMS data related to the different centrifugation protocols.

Conclusion

Already minor differences in plasma centrifugation can significantly influence metabolomic patterns and potentially bias metabolomics studies.

     

Determination and optimization of a strong promoter element from <Emphasis Type="Italic">Bacillus amyloliquefaciens</Emphasis> by using a promoter probe vector

Objective

To construct a promoter probe vector, pBE-bgaB, to screen strong promoters from Bacillus amyloliquefaciens.

Results

266 colonies containing active promoter elements from the genomic DNA of B. amyloliquefaciens were identified. Among these, promoter P41 exhibited the strongest β-Gal activity in Escherichia coli and B. amyloliquefaciens. Sequence analysis showed that promoter P41 contained P _ykuN , a ykuN gene encoding flavodoxin. Optimization of the ribosome-binding site from P41 to P₃₈₂ improved β-Gal activity by ~ 200%.

Conclusion

A new strong promoter for protein expression and genetic engineering of Bacillus species.

     

Fungal Keratitis Secondary to <Emphasis Type="Italic">Trametes betulina</Emphasis>: A Case Report and Review of Literature

Purpose

We report the first case of human infection and keratitis secondary to Trametes betulina, a rare filamentous fungus.

Methods

Clinical examination including external and slit-lamp examination and corneal scrapings with microbiologic evaluation were performed on a patient with chronic allergic conjunctivitis, entropion and a long-standing corneal ulcer resistant to treatment.

Results

The culture from the corneal scraping revealed a basidiomycetous fungus which was submitted for identification. DNA extraction with sequencing and analysis of the ITS and D1/D2 regions were performed on the isolate and demonstrated 100% similarity to Lenzites betulina/Trametes betulina. Susceptibility testing demonstrated potent in vitro activity of voriconazole (MIC < 0.03 μg/ml). The patient was treated with voriconazole, and the corneal ulcer and infiltrate resolved. The infection resulted in corneal thinning and a dense central corneal scar. Penetrating keratoplasty was performed 5 months after diagnosis and treatment and revealed stromal scarring without fungal elements.

Conclusion

This is the first reported case of keratitis caused by Trametes betulina. This organism should be considered in the differential diagnosis for rare filamentous fungal keratitis and its treatment with voriconazole also noted.

     

Metabolic response of porcine colon explants to in vitro infection by <Emphasis Type="Italic">Brachyspira hyodysenteriae</Emphasis>: a leap into disease pathophysiology

Introduction

Swine dysentery caused by Brachyspira hyodysenteriae is a production limiting disease in pig farming. Currently antimicrobial therapy is the only treatment and control method available.

Objective

The aim of this study was to characterize the metabolic response of porcine colon explants to infection by B. hyodysenteriae.

Methods

Porcine colon explants exposed to B. hyodysenteriae were analyzed for histopathological, metabolic and pro-inflammatory gene expression changes.

Results

Significant epithelial necrosis, increased levels of l-citrulline and IL-1α were observed on explants infected with B. hyodysenteriae.

Conclusions

The spirochete induces necrosis in vitro likely through an inflammatory process mediated by IL-1α and NO.

     

Degradation of carbazole,dibenzothiophene and polyaromatic hydrocarbons by recombinant <Emphasis Type="Italic">Rhodococcus</Emphasis> sp.

Objectives

With the view of designing a single biocatalyst for biorefining, carbazole dioxygenase was cloned from Pseudomonas sp. and expressed in Rhodococcus sp.

Results

The recombinant, IGTS8, degraded both carbazole and dibenzothiophene at 400 mg/l in 24 h. Maximum carbazole degradation was in 1:1 (v/v) hexadecane/aqueous phase. Anthracene, phenanthrene, pyrene, fluoranthene and fluorine were also degraded without affecting the aliphatic component.

Conclusions

Recombinant Rhodococcus sp. IGTS8 can function as a single biocatalyst for removing major contaminants of fossil fuels viz. dibenzothiophene, carbazole and polyaromatic compounds.