Isolation of facultatively anaerobic soil bacteria from Ny-Ålesund, Svalbard

Application of phosphorus amendments reduces metal uptake and increases yield of Oryza saliva L. (rice) in Cd/Cu-contaminated paddy field

To alleviate worldwide food safety issues caused by metal contamination, an easily available material is urgently needed for extensive application. In this study, calcium magnesium phosphate fertiliser (Pcm) was applied to a Cd/Cu co-contaminated paddy field in comparison with limestone and organic fertiliser. The results showed that only Pcm is effective in simultaneously reducing Cd uptake by 56.7% and Cu uptake by 36.2% in Oryza saliva L. (rice). The rice yield, reduced mainly by Cu, also increased by 30.1% with respect to the enhancement of soil pH, cation exchange capacity and availability of phosphorus, as well as the reduction in availabilities of Cd and Cu. Additionally, Pcm dramatically shaped the bacterial community structure, with Proteobacteria and Firmicutes predominant in the soils. The beneficial genera Exiguobacterium, Citrobacter, and Acinetobacter, which are vital for phosphate dissolution and Cd/Cu immobilisation, were also enriched. The results demonstrated that the application of Pcm at 0.4% (w:w) was able to enhance both crop quantity and quality in Cd/Cu co-contaminated paddy fields by reducing Cu/Cd availability, promoting rice yield, and reshaping bacterial community structures.

Alkaline amendments improve the health of soils degraded by metal contamination and acidification: Crop performance and soil bacterial community responses

Soil degradation due to heavy metal contamination and acidification has negative effects on soil health and crop growth. Many previous studies have tried to improve the growth of crops and decrease their metal uptake. The recovery of soil health, however, has rarely been focused in soil remediation. In this study, a pot trial was conducted with lettuce (Lactuca sativa L.) growing in heavy metal contaminated and acidic soils, to examine the effects of alkaline amendments (limestone, LS; calcium magnesium phosphate fertilizer, Pcm) and organic amendments (cow manure compost, CMC; biochar, BC) on the growth of lettuce and on the availability of heavy metals, enzyme activities, and bacterial community structures in the soils. The results showed that, in comparison with the CMC and BC treatments, LS and Pcm were more effective at improving lettuce growth and reducing metal concentrations in shoots. Urease and catalase activities in LS and Pcm amended soils were consistently higher than in those with CMC and BC. Additionally, the alkaline amendments dramatically improved the bacterial diversity and shaped more favorable bacterial community structures. Proteobacteria and Gemmatimonadetes were predominant in soils amended with alkaline treatments. The beneficial bacterial genera Gemmatimonas and f_Gemmatimonadaceae, which are vital for phosphate dissolution, microbial nitrogen metabolism, and soil respiration, were also enriched. The results suggest that alkaline amendments were superior to organic amendments, and thus may be useful for the future recovery of soil functions and health under heavy metal contamination and low pH.

Physiological Diversity of Spitsbergen Soil Microbial Communities Suggests Their Potential as Plant Growth-Promoting Bacteria

The objective of the study was to assess the physiological diversity and metabolic activity of the soil bacterial communities inhabiting Spitsbergen soils in search of bacterial abilities facilitating plant growth promotion. In the soil, the total number of culturable microorganisms, the number of their individual physiological groups (including Siderophore Synthesizing; SSB and Phosphate Solubilizing Bacteria; PSB), the dehydrogenase (DH) activity, and the ability to utilize sources of C, N, P (EcoPlate) were analysed. In bacterial isolates, siderophores production, ACC (1-aminocyclopropane-1-carboxylate) deaminase (ACCD) activity, IAA (indole-3-acetic acid) synthesis were examined. The isolates were applied to the seeds of Phaseolus coccineus regarding their germination and root length. The results showed differences between copio- and oligotrophic bacteria. A usually high number of SSB was accompanied by the raised number of PSB. A bigger number of SSB was connected with low values of Fe in the soil. High DH activity was assisted by greater number of copio- and oligotrophic bacteria, raised average well color development value, and N and C contents in the soil. Germination index was more alike relative seed germination than relative root growth. IAA concentration and ACCD activity were conversely related. Synthesis of siderophores was matched with ACCD activity and its high level was combined with elevated germination index. In spite of different localization of soil samples, some isolates proved similar traits of activity. Distinct affiliation of isolates and their various localizations were displayed. Among all isolates tested, some possessed one main trait of activity, but most of them had two or more significant features for potential plant growth stimulation. These isolates could be an important source of useful bacteria.

Dynamics of microbial communities and CO2 and CH4 fluxes in the tundra ecosystems of the changing Arctic

Arctic tundra ecosystems are rapidly changing due to the amplified effects of global warming within the northern high latitudes. Warming has the potential to increase the thawing of the permafrost and to change the landscape and its geochemical characteristics, as well as terrestrial biota. It is important to investigate microbial processes and community structures, since soil microorganisms play a significant role in decomposing soil organic carbon in the Arctic tundra. In addition, the feedback from tundra ecosystems to climate change, including the emission of greenhouse gases into the atmosphere, is substantially dependent on the compositional and functional changes in the soil microbiome. This article reviews the current state of knowledge of the soil microbiome and the two most abundant greenhouse gas (CO₂ and CH₄) emissions, and summarizes permafrost thaw-induced changes in the Arctic tundra. Furthermore, we discuss future directions in microbial ecological research coupled with its link to CO₂ and CH₄ emissions.

Clomazone influence soil microbial community and soil nitrogen cycling

We designed an indoor mesocosm experiment to investigate the long-term effects of exposure to clomazone, a widely used herbicide, on soil microbial communities and their nitrogen (N) cycling functions. Clomazone was applied to two typical soils from China at three concentrations: 0.8 (the recommended dosage), 8 and 80 mg kg^-1 soil dry weight, and the mix was incubated for 90 days. Samples were removed periodically for assay with several techniques. The half-lives of clomazone in this experiment were 11-126 d. Results were significant only for the highest clomazone concentration. Next-generation sequencing of the 16S and 18S rDNA genes revealed that bacterial diversity significantly decreased whereas fungal abundance increased after day 60 but with no detectable effect on the microbial community. Hierarchical cluster and principal coordinates analysis revealed that the bacterial community structure was negatively impacted. Linear discriminant analysis of effect size identified Sphingomonas and Arthrobacter as the predominant bacterial species. Finally, we measured soil NH₄⁺ and NO₃^- concentrations and used real-time PCR to analyze the abundance of the N-cycling genes, nifH and amoA. In the first 30 days, the NO₃^--N content and the number of ammonia-oxidizing bacteria increased. N₂-fixing bacteria were inhibited after 60 days, but the NH₄⁺-N concentration remained unchanged and was likely provided by ammoniation.

Microbial ecology of full-scale wastewater treatment systems in the Polar Arctic Circle: Archaea, Bacteria and Fungi

Seven full-scale biological wastewater treatment systems located in the Polar Arctic Circle region in Finland were investigated to determine their Archaea, Bacteria and Fungi community structure, and their relationship with the operational conditions of the bioreactors by the means of quantitative PCR, massive parallel sequencing and multivariate redundancy analysis. The results showed dominance of Archaea and Bacteria members in the bioreactors. The activated sludge systems showed strong selection of Bacteria but not for Archaea and Fungi, as suggested by diversity analyses. Core OTUs in influent and bioreactors were classified as Methanobrevibacter, Methanosarcina, Terrestrial Group Thaumarchaeota and unclassified Euryarchaeota member for Archaea; Trichococcus, Leptotrichiaceae and Comamonadaceae family, and Methylorosula for Bacteria and Trichosporonaceae family for Fungi. All influents shared core OTUs in all domains, but in bioreactors this did not occur for Bacteria. Oligotype structure of core OTUs showed several ubiquitous Fungi oligotypes as dominant in sewage and bioreactors. Multivariate redundancy analyses showed that the majority of core OTUs were related to organic matter and nutrients removal. Also, there was evidence of competition among Archaea and Fungi core OTUs, while all Bacteria OTUs were positively correlated among them. The results obtained highlighted interesting features of extremely cold temperature bioreactors.

Improved in situ saccharification of cellulose pretreated by dimethyl sulfoxide/ionic liquid using cellulase from a newly isolated Paenibacillus sp. LLZ1

A cellulase producing strain was newly isolated from soil samples and identified as Paenibacillus sp. LLZ1. A novel aqueous-dimethyl sulfoxide (DMSO)/1-ethyl-3-methylimidazolium diethyl phosphate ([Emin]DEP)-cellulase system was designed and optimized. In the pretreatment, DMSO was found to be a low-cost substitute of up to 70% ionic liquid to enhance the cellulose dissolution. In the enzymatic saccharification, the optimum pH and temperature of the Paenibacillus sp. LLZ1 cellulase were identified as 6.0 and 40°C, respectively. Under the optimized reaction condition, the conversion of microcrystalline cellulose and bagasse cellulose increased by 39.3% and 37.6%, compared with unpretreated cellulose. Compared to current methods of saccharification, this new approach has several advantages including lower operating temperature, milder pH, and less usage of ionic liquid, indicating a marked progress in environmental friendly hydrolysis of biomass-based materials.

Optimization of isolation and cultivation of bacterial endophytes through addition of plant extract to nutrient media

Many endophytes have beneficial effects on plants and can be exploited in biotechnological applications. Studies hypothesize that only 0.001-1% of all plant-associated bacteria are cultivable. Moreover, even after successful isolations, many endophytic bacteria often show reduced regrowth capacity. This research aimed to optimize isolation processes and culturing these bacteria afterwards. We compared several minimal and complex media in a screening. Beside the media themselves, two gelling agents and adding plant extract to media were investigated to enhance the number and diversity of endophytes as well as the growth capacity when regrown after isolation. In this work, 869 medium delivered the highest numbers of cultivable bacteria, as well as the highest diversity. When comparing gelling agents, no differences were observed in the numbers of bacteria. Adding plant extract to the media lead to a slight increase in diversity. However, when adding plant extract to improve the regrowth capacity, sharp increases of viable bacteria occurred in both rich and minimal media.

Degradation and detoxification of methylene blue dye adsorbed on water hyacinth in semi continuous anaerobic–aerobic bioreactors by novel microbial consortium-SB

Combinatorial adsorption–biodegradation treatment of textile wastewater provides a cost effective and ecofriendly alternative to conventional physicochemical treatment methods.