Diversity and composition of microbial communities in Jinsha earthen site under different degree of deterioration.

Earthen sites are the important cultural heritage that carriers of human civilization and contains abundant history information. Microorganisms are one of important factors causing the deterioration of cultural heritage. However, little attention has been paid to the role of biological factors on the deterioration of earthen sites at present. In this study, microbial communities of Jinsha earthen site soils with different deterioration types and degrees as well as related to environmental factors were analyzed. The results showed that the concentrations of Mg2+ and SO42- were higher in the severe deterioration degree soils than in the minor deterioration degree soils. The Chao1 richness and Shannon diversity indices of bacteria in different type deterioration were higher in the summer than in the winter; the Chao1 and Shannon indices of fungi were lower in the summer. The differences in bacterial and fungal communities were associated with differences in Na+, K+, Mg2+ and Ca2+ contents. Based on both the relative abundances in amplicon sequencing and isolated strains, the bacterial phyla Actinobacteria, Firmicutes and Proteobacteria, and the Ascomycota genera Aspergillus, Cladosporium and Penicillium were common in all soils. The OTUs enriched in the severe deterioration degree soils were mostly assigned to Actinobacteria and Proteobacteria, whereas the Firmicutes OTUs differentially abundant in the severe deterioration degree were all depleted. All bacterial isolates produced alkali, implying that the deterioration on Jinsha earthen site may be accelerated through alkali production. The fungal isolates included both alkali and acid producing strains. The fungi with strong ability to produce acid were mainly from the severe deterioration degree samples and were likely to contribute to the deterioration. Taken together, the interaction between soil microbial communities and environment may affect the soil deterioration, accelerate the deterioration process and threaten the long-term preservation of Jinsha earthen site.

Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda.

The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.

Ciceribacter sichuanensis sp. nov., a plant growth promoting rhizobacterium isolated from root nodules of soybean in Sichuan, China.

The fast-growing rhizobia-like strains S101T and S153, isolated from root nodules of soybean (Glycine max) in Sichuan, People's Republic of China, underwent characterization using a polyphasic taxonomy approach. The strains exhibited growth at 20-40 °C (optimum, 28 °C), pH 4.0-10.0 (optimum, pH 7.0) and up to 2.0% (w/v) NaCl (optimum, 0.01%) on Yeast Mannitol Agar plates. The 16S rRNA gene of strain S101T showed 98.4% sequence similarity to the closest type strain, Ciceribacter daejeonense L61T. Major cellular fatty acids in strain S101T included summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. The predominant quinone was ubiquinone-10. The polar lipids of strain S101T included diphosphatidylglycerol, phosphatidylglycerol, phosphatidylmethyl ethanolamine, phosphatidyl ethanolamine, amino phospholipid, unidentified phosphoglycolipid and unidentified amino-containing lipids. The DNA G + C contents of S101T and S153 were 61.1 and 61.3 mol%, respectively. Digital DNA-DNA hybridization relatedness and average nucleotide identity values between S101T and C. daejeonense L61T were 46.2% and 91.4-92.2%, respectively. In addition, strain S101T promoted the growth of soybean and carried nitrogen fixation genes in its genome, hinting at potential applications in sustainable agriculture. We propose that strains S101T and S153 represent a novel species, named Ciceribacter sichuanensis sp. nov., with strain S101T as the type strain (= CGMCC 1.61309 T = JCM 35649 T).

Bacterial community in the buckwheat rhizosphere responds more sensitively to single microplastics in lead-contaminated soil compared to the arbuscular mycorrhizal fungi community.

Soil pollution by microplastics (MPs), defined as plastic particles <5 mm, and heavy metals is a significant environmental issue. However, studies on the co-contamination effects of MPs and heavy metals on buckwheat rhizosphere microorganisms, especially on the arbuscular mycorrhizal fungi (AMF) community, are limited. We introduced low (0.01 g kg-1) and high doses of lead (Pb) (2 g kg-1) along with polyethylene (PE) and polylactic acid (PLA) MPs, both individually and in combination, into soil and assessed soil properties, buckwheat growth, and rhizosphere bacterial and AMF communities in a 40-day pot experiment. Notable alterations were observed in soil properties such as pH, alkaline hydrolyzable nitrogen (AN), and the available Pb (APb). High-dose Pb combined with PLA-MPs hindered buckwheat growth. Compared to the control, bacterial Chao1 richness and Shannon diversity were lower in the high dose Pb with PLA treatment, and differentially abundant bacteria were mainly detected in the high Pb dose treatments. Variations in bacterial communities correlated with APb, pH and AN. Overall, the AMF community composition remained largely consistent across all treatments. This phenomenon may be due to fungi having lower nutritional demands than bacteria. Stochastic processes played a relatively important role in the assembly of both bacterial and AMF communities. In summary, MPs appeared to amplify both the positive and negative effects of high Pb doses on the buckwheat rhizosphere bacteria.

Bacterial community drives soil organic carbon transformation in vanadium titanium magnetite tailings through remediation using Pongamia pinnata.

With continuous mine exploitation, regional ecosystems have been damaged, resulting in a decline in the carbon sink capacity of mining areas. There is a global shortage of effective soil ecological restoration techniques for mining areas, especially for vanadium (V) and titanium (Ti) magnetite tailings, and the impact of phytoremediation techniques on the soil carbon cycle remains unclear. Therefore, this study aimed to explore the effects of long-term Pongamia pinnata remediation on soil organic carbon transformation of V-Ti magnetite tailing to reveal the bacterial community driving mechanism. In this study, it was found that four soil active organic carbon components (ROC, POC, DOC, and MBC) and three carbon transformation related enzymes (S-CL, S-SC, and S-PPO) in vanadium titanium magnetite tailings significantly (P < 0.05) increased with P. pinnata remediation. The abundance of carbon transformation functional genes such as carbon degradation, carbon fixation, and methane oxidation were also significantly (P < 0.05) enriched. The network nodes, links, and modularity of the microbial community, carbon components, and carbon transformation genes were enhanced, indicating stronger connections among the soil microbes, carbon components, and carbon transformation functional genes. Structural equation model (SEM) analysis revealed that the bacterial communities indirectly affected the soil organic carbon fraction and enzyme activity to regulate the soil total organic carbon after P. pinnata remediation. The soil active organic carbon fraction and free light fraction carbon also directly regulated the soil carbon and nitrogen ratio by directly affecting the soil total organic carbon content. These results provide a theoretical reference for the use of phytoremediation to drive soil carbon transformation for carbon sequestration enhancement through the remediation of degraded ecosystems in mining areas.

Chelativorans petroleitrophicus sp. nov., a paraffin oil-degrading bacterium isolated from a mixture of oil-based drill cuttings and paddy soil.

We isolated a paraffin oil-degrading bacterial strain from a mixture of oil-based drill cutting and paddy soil, and characterized the strain using a polyphasic approach. The Gram-positive, aerobic, rod-shaped and non-spore-forming strain (SCAU 2101T) grew optimally at 50 °C, pH 7.0 and 0.5 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA gene sequence indicated that the strain represented a distinct clade in the genus Chelativorans, neighbouring Chelativorans intermedius LMG 28482T (97.1 %). The genome size and DNA G+C content of the strain were 3 969 430 bp and 63.1 mol%, respectively. Whole genome based phylogenomic analyses showed that the average nucleotide identity and digital DNA-DNA hybridization values between strain SCAU 2101T and C. intermedius LMG 28482T were 77.5 and 21.2 %, respectively. The major respiratory quinone was Q-10. The dominant fatty acids were C19 : 0 cyclo ω8c (50.6 %), summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c; 22.5 %) and C18 : 0 (13.8 %). The polar lipids of the strain included phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidylglycerol, phosphatidylcholine and diphosphatidylglycerol. Based on the results, strain SCAU 2101T was considered to represent a novel species in the genus Chelativorans, for which the name Chelativorans petroleitrophicus sp. nov. is proposed. The type strain is SCAU 2101T (= CCTCC AB 2021125T=KCTC 92067T).

Organic Fertilizers Shape Soil Microbial Communities and Increase Soil Amino Acid Metabolites Content in a Blueberry Orchard.

The decline in soil nutrients is becoming a major concern of soil degradation. The possibility of using organic waste as a soil additive to increase nutrients and essential components is significant in soil quality protection and waste management. The aim of this study was to investigate the effects of composted spent mushroom substrate (MS), giant panda feces (PF), and cattle manure (CM) as organic fertilizers in soil microbial communities and metabolites in blueberry orchard in China, which were measured by using high-throughput sequencing and gas chromatography-mass spectrometry (GC-MS)-based metabolomics. Altogether, 45.66% of the bacterial operational taxonomic units (OTUs) and 9.08% of the fungal OTUs were detected in all treatments. Principal coordinates analysis demonstrated that the bacterial and fungal communities in MS and PF treatments were similar, whereas the communities in the not-organic fertilized control (CK) were significantly different from those in the organic fertilizer treatments. Proteobacteria, Acidobacteria, and Bacteroidetes were the dominant bacterial phyla, and Basidiomycota, Ascomycota, and Mortierellomycota the dominant fungal phyla. Redundancy analysis indicated that pH and available potassium were the main factors determining the composition of microbial communities. The fungal genera Postia, Cephalotrichum, and Thermomyces increased in organic fertilizer treatments, and likely promoted the degradation of organic fertilizers into low molecular-weight metabolites (e.g., amino acids). PCA and PLS-DA models showed that the metabolites in CK were different from those in the other three treatments, and those in CM were clearly different from those in MS and PF. Co-occurrence network analysis showed that several taxa correlated positively with amino acid contents. The results of this study provide new insights into organic waste reutilization and new directions for further studies.

Response of soil microbial community structure and function to different altitudes in arid valley in Panzhihua, China.

BACKGROUND: Altitude affects biodiversity and physic-chemical properties of soil, providing natural sites for studying species distribution and the response of biota to environmental changes. We sampled soil at three altitudes in an arid valley, determined the physic-chemical characteristics and microbial community composition in the soils, identified differentially abundant taxa and the relationships between community composition and environmental factors. RESULTS: The low, medium and high altitudes were roughly separated based on the physic-chemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in soil pH, temperature, and SOC, moisture, TN, TP, AN, AP and SMBC contents. The contents of organic and microbial biomass C, total and available N and available P, and the richness and diversity of the microbial communities were lowest in the medium altitude. The relative abundances of phyla Proteobacteria, Gemmatimonadetes, Actinobacteria and Acidobacteria were high at all altitudes. The differentially abundant amplified sequence variants (ASVs) were mostly assigned to Proteobacteria and Acidobacteria. The highest number of ASVs characterizing altitude were detected in the high altitude. However, the predicted functions of the communities were overlapping, suggesting that the contribution of the communities to soil processes changed relatively little along the altitude gradient. CONCLUSIONS: The low, medium and high altitudes were roughly separated based on the physicochemical characteristics and clearly separated based on the microbial community composition. The differences in community composition were associated with differences in soil pH, temperature, and SOC, moisture, TN, TP, AN, AP and SMBC contents.

Antimicrobial resistance of Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp. isolated from the feces of giant panda.

BACKGROUND: Escherichia coli, Enterobacter spp., Klebsiella pneumoniae and Enterococcus spp., common gut bacteria in giant pandas, include opportunistic pathogens. The giant panda is an endangered species, classified as vulnerable by the World Wildlife Foundation. Continuous monitoring for the emergence of antimicrobial resistance (AMR) among bacterial isolates from giant pandas is vital not only for their protection but also for public health. RESULTS: A total of 166 E. coli, 68 Enterobacter spp., 116 K. pneumoniae and 117 Enterococcus spp. isolates were collected from fecal samples of 166 giant pandas. In the antimicrobial susceptibility tests, 144 E. coli isolates, 66 Enterobacter spp. isolates, 110 K. pneumoniae isolates and 43 Enterococcus spp. isolates were resistant to at least one antimicrobial. The resistant isolates carried antimicrobial resistance genes (ARGs), including sul3, blaTEM, blaSHV and tetA. The differences in the prevalence of the bla types implied that the genetic basis for ß-lactam resistance among the E. coli, Enterobacter spp. and K. pneumoniae isolates was different. The strain K. pneumoniae K85 that was resistant to sixteen antimicrobials was selected for whole genome sequencing. The genome contained Col440I, IncFIBK and IncFIIK plasmids and altogether 258 ARGs were predicted in the genome; 179 of the predicted ARGs were efflux pump genes. The genetic environment of the ß-lactamase genes blaCTX-M-3 and blaTEM-1 in the K. pneumoniae K85 genome was relatively similar to those in other sequenced K. pneumoniae genomes. In comparing the giant panda age groups, the differences in the resistance rates among E. coli, K. pneumoniae and Enterobacter spp. isolates suggested that the infections in giant pandas of different age should be treated differently. CONCLUSIONS: Antimicrobial resistance was prevalent in the bacterial isolates from the giant pandas, implying that the gut bacteria may pose serious health risks for captive giant pandas. The resistance genes in the genome of K. pneumoniae K85 were associated with insertion sequences and integron-integrase genes, implying a potential for the further spread of the antimicrobial resistance.

Changes in the taxonomic and functional structures of microbial communities during vegetable waste mixed silage fermentation.

Silage fermentation, a sustainable method of using vegetable waste resources, is a complex process driven by a variety of microorganisms. We used lettuce waste as the main raw material for silage, analyzed changes in the physicochemical characteristics and bacterial community composition of silage over a 60-day fermentation period, identified differentially abundant taxa, predicted the functional profiles of bacterial communities, and determined the associated effects on the quality of silage. The largest changes occurred during the early stages of silage fermentation. Changes in the physicochemical characteristics included a decrease in pH and an increase in the ammonia nitrogen to total nitrogen ratio and lactic acid content. The number of lactic acid bacteria (LAB) increased, while molds, yeasts, and aerobic bacteria decreased. The bacterial communities and their predicted functions on day 0 were different from those on day 7 to day 60. The relative abundances of phylum Firmicutes and genus Lactobacillus increased. Nitrite and nitrate ammonification were more prevalent after day 0. The differences in the predicted functions were associated with differences in pH and amino acid, protein, carbohydrate, NH3-N, ether extract, and crude ash contents.

Changes in soil microbial communities at Jinsha earthen site are associated with earthen site deterioration.

BACKGROUND: Earthen sites are immobile cultural relics and an important part of cultural heritage with historical, artistic and scientific values. The deterioration of features in earthen sites result in permanent loss of cultural information, causing immeasurable damage to the study of history and culture. Most research on the deterioration of earthen sites has concentrated on physicochemical factors, and information on microbial communities in earthen sites and their relationship with the earthen site deterioration is scarce. We used high-throughput sequencing to analyze bacterial and fungal communities in soils from earthen walls with different degree of deterioration at Jinsha earthen site to characterize the microbial communities and their correlation with environmental factors, and to compare microbial community structures and the relative abundances of individual taxa associated with different degree of deterioration for identifying possible marker taxa. RESULTS: The relative abundances of Proteobacteria and Firmicutes were higher and that of Actinobacteria lower with higher degree of deterioration. At the genus level, the relative abundances of Rubrobacter were highest in all sample groups except in the most deteriorated samples where that of Bacteroides was highest. The relative abundance of the yeast genus Candida was highest in the severely deteriorated sample group. The bacterial phylum Bacteroidetes and genus Bacteroides, and fungal class Saccharomycetes that includes Candida sp. were specific for the most deteriorated samples. For both bacteria and fungi, the differences in community composition were associated with differences in EC, moisture, pH, and the concentrations of NH4+, K+, Mg2+, Ca2+ and SO42-. CONCLUSION: The microbial communities in soil with different degree of deterioration were distinctly different, and deterioration was accompanied with bigger changes in the bacterial than in the fungal community. In addition, the deteriorated soil contained higher concentrations of soluble salts. Potentially, the accumulation of Bacteroides and Candida plays an important role in the deterioration of earthen features. Further work is needed to conclude whether controlling the growth of the bacteria and fungi with high relative abundances in the deteriorated samples can be applied to alleviate deterioration.

Pongamia pinnata inoculated with Bradyrhizobium liaoningense PZHK1 shows potential for phytoremediation of mine tailings.

Mine tailings contain high concentrations of metal contaminants and only little nutrients, making the tailings barren for decades after the mining has been terminated. Effective phytoremediation of mine tailings calls for deep-rooted, metal accumulating, and soil fertility increasing plants with tolerance against harsh environmental conditions. We assessed the potential of the biofuel leguminous tree Pongamia pinnata inoculated with plant growth promoting rhizobia to remediate iron-vanadium-titanium oxide (V-Ti magnetite) mine tailing soil by pot experiment and in situ remediation test. A metal tolerant rhizobia strain PZHK1 was isolated from the tailing soil and identified as Bradyrhizobium liaoningense by phylogenetic analysis. Inoculation with PZHK1 increased the growth of P. pinnata both in V-Ti magnetite mine tailings and in Ni-contaminated soil. Furthermore, inoculation increased the metal accumulation capacity and superoxide dismutase activity of P. pinnata. The concentrations of Ni accumulated by inoculated plants were higher than the hyperaccumulator threshold. Inoculated P. pinnata accumulated high concentration of Fe, far exceeding the upper limit (1000 mg kg-1) of Fe in plant tissue. In summary, P. pinnata-B. liaoningense PZHK1 symbiosis showed potential to be applied as an effective phytoremediation technology for mine tailings and to produce biofuel feedstock on the marginal land.

Isolation and antimicrobial activities of actinobacteria closely associated with liquorice plants Glycyrrhiza glabra L. and Glycyrrhiza inflate BAT. in Xinjiang, China.

A total of 218 actinobacteria strains were isolated from wild perennial liquorice plants Glycyrrhiza glabra L. and Glycyrrhiza. inflate BAT. Based on morphological characteristics, 45 and 32 strains from G. inflate and G. glabra, respectively, were selected for further analyses. According to 16S rRNA sequence analysis, most of the strains belonged to genus Streptomyces and a few strains represented the rare actinobacteria Micromonospora, Rhodococcus and Tsukamurella. A total of 39 strains from G. inflate and 27 strains from G. glabra showed antimicrobial activity against at least one indicator organism. The range of the antimicrobial activity of the strains isolated from G. glabra and G. inflate was similar. A total of 34 strains from G. inflate and 29 strains from G. glabra carried at least one of the genes encoding polyketide synthases, non-ribosomal peptide synthetase and FADH2-dependent halogenase. In the type II polyketide synthase KSα gene phylogenetic analysis, the strains were divided into two major clades: one included known spore pigment production-linked KSα sequences and other sequences were linked to the production of different types of aromatic polyketide antibiotics. Based on the antimicrobial range, the isolates that carried different KSα types were not separated from each other or from the isolates that did not carry KSα. The incongruent phylogenies of 16S rRNA and KSα genes indicated that the KSα genes were possibly horizontally transferred. In all, the liquorice plants were a rich source of biocontrol agents that may produce novel bioactive compounds.

Divergent genes in potential inoculant Sinorhizobium strains are related to DNA replication, recombination, and repair.

To serve as inoculants of legumes, nitrogen-fixing rhizobium strains should be competitive and tolerant of diverse environments. We hybridized the genomes of symbiotically efficient and salt tolerant Sinorhizobium inoculant strains onto the Sinorhizobium meliloti Rm1021 microarray. The number of variable genes, that is, divergent or putatively multiplied genes, ranged from 503 to 1556 for S. meliloti AK23, S. meliloti STM 1064 and S. arboris HAMBI 1552. The numbers of divergent genes affiliated with the symbiosis plasmid pSymA and related to DNA replication, recombination and repair were significantly higher than expected. The variation was mainly in the accessory genome, implying that it was important in shaping the adaptability of the strains.

A combination of omics-based analyses to elucidate the effect of NaCl concentrations on the metabolites and microbial dynamics during the ripening fermentation of Pixian-Douban.

The study investigated the effect of different sodium chloride (NaCl) concentrations (10%, 15%, and 20%) on the ripening fermentation of Pixian-Douban, a traditional fermented condiment. The results showed that NaCl affected the dynamics of physicochemical parameters, volatile components, fatty acids, amino metabolites, organic acids, and microbial composition, and their dynamic modes were different. After 253 days fermentation, the 10% NaCl Pixian-Douban had significantly (p < 0.05) higher levels of total organic acids (20,308.25 mg/kg), amino metabolites (28,144.96 mg/kg), and volatiles (3.36 mg/kg) compared to 15% and 20% NaCl Pixian-Douban. Notably, the possible health risk associated with high concentration of biogenic amines in 10% NaCl Pixian-Douban is of concern. Moreover, correlation analyses indicated that the effect of NaCl on the quality of Pixian-Douban may be mainly related to bacteria. This study deepens the knowledge about the role of NaCl in ripening fermentation of Pixian-Douban and contributes to develop low-NaCl Pixian-Douban product.

Combined transcriptomic and metabolomic analysis revealed that pH changes affected the expression of carbohydrate and ribosome biogenesis-related genes in Aspergillus niger SICU-33.

The process of carbohydrate metabolism and genetic information transfer is an important part of the study on the effects of the external environment on microbial growth and development. As one of the most significant environmental parameters, pH has an important effect on mycelial growth. In this study, the effects of environmental pH on the growth and nutrient composition of Aspergillus niger (A. niger) filaments were determined. The pH values of the medium were 5, 7, and 9, respectively, and the molecular mechanism was further investigated by transcriptomics and metabolomics methods. The results showed that pH 5 and 9 significantly inhibited filament growth and polysaccharide accumulation of A. niger. Further, the mycelium biomass of A. niger and the crude polysaccharide content was higher when the medium's pH was 7. The DEGs related to ribosome biogenesis were the most abundant, and the downregulated expression of genes encoding XRN1, RRM, and RIO1 affected protein translation, modification, and carbohydrate metabolism in fungi. The dynamic changes of pargyline and choline were in response to the oxidative metabolism of A. niger SICU-33. The ribophorin_I enzymes and DL-lactate may be important substances related to pH changes during carbohydrate metabolism of A.niger SICU-33. The results of this study provide useful transcriptomic and metabolomic information for further analyzing the bioinformatic characteristics of A. niger and improving the application in ecological agricultural fermentation.

Transcriptomic analysis and carbohydrate metabolism-related enzyme expression across different pH values in Rhizopus delemar.

Introduction: pH is one of the important factors affecting the growth and performance of microorganisms. Methods: We studied the pH response and plant growth-promoting (PGP) ability of Rhizopus delemar using cultivation experiments and transcriptomics, and verified the expression profiles using quantitative real-time PCR. Results: pH affected the growth and PGP properties of R. delemar. At pH 7, the growth rate of R. delemar was rapid, whereas pH 4 and 8 inhibited mycelial growth and PGP ability, respectively. In the pot experiment, the plant height was the highest at pH 7, 56 cm, and the lowest at pH 4 and pH 5, 46.6 cm and 47 cm, respectively. Enzyme activities were highest at pH 6 to pH 7. Enzyme activities were highest at pH 6 to pH 7. Among the 1,629 differentially expressed genes (DEGs), 1,033 genes were up-regulated and 596 were down-regulated. A total of 1,623 DEGs were annotated to carbohydrate-active enzyme coding genes. Discussion: The PGP characteristics, e.g., Phosphorus solubilization ability, of R. delemar were strongest at pH 7. The results provide useful information regarding the molecular mechanism of R. delemar pH response.

Symbiotic efficiency and phylogeny of the rhizobia isolated from Leucaena leucocephala in arid-hot river valley area in Panxi, Sichuan, China.

In search of effective nitrogen-fixing strains for inoculating Leucaena leucocephala, we assessed the symbiotic efficiency of 41 rhizobial isolates from root nodules of L. leucocephala growing in the arid-hot river valley area in Panxi, China. The genetic diversity of the isolates was studied by analyzing the housekeeping genes 16S rRNA and recA, and the symbiotic genes nifH and nodC. In the nodulation and symbiotic efficiency assay, only 11 of the 41 isolates promoted the growth of L. leucocephala while the majority of the isolates were ineffective in symbiotic nitrogen fixation. Furthermore, one fourth of the isolates had a growth slowing effect on the host. According to the 16S rRNA and recA gene analyses, most of the isolates were Ensifer spp. The remaining isolates were assigned to Rhizobium, Mesorhizobium and Bradyrhizobium. The sequence analyses indicated that the L. leucocephala rhizobia had undergone gene recombination. In contrast to the promiscuity observed as a wide species distribution of the isolates, the results implied that L. leucocephala is preferentially nodulated by strains that share common symbiosis genes. The symbiotic efficiency was not connected to chromosomal background of the symbionts and isolates carrying a similar nifH or nodC showed totally different nitrogen fixation efficiency.

Polyphasic characterization of rhizobia isolated from Leucaena leucocephala from Panxi, China.

Leucaena leucocephala was introduced into Panxi, Sichuan, China, in the 1980s and 1990s for afforestation and preventing water loss and soil erosion in this area. The co-introduction of rhizobial symbionts of introduced plants has drawn attention since they may influence local soil communities. We studied the phylogenetic position of the L. leucocephala isolates and assessed if the rhizobia were introduced together with the host to Panxi, Sichuan, China. The glnII and atpD genes of fifteen representative isolates were sequenced and analyzed, and applied multilocus sequence analyses in which the housekeeping genes recA, glnII and atpD were included. Furthermore, we estimated the within species diversity directly with 23S rDNA and IGS RFLP and indirectly through phenotypic analysis of forty L. leucocephala isolates. The isolates represented seven species and 38 diversified strains in the genera Ensifer, Mesorhizobium, Bradyrhizobium and Rhizobium. The within species diversity of the Ensifer isolates was large, proposing a potential to occupy novel niches. There was not conclusive evidence to show that any of the strains would have been co-introduced with L. leucocephala. On the contrary, we came to a conclusion that the possible introduction should not be inferred from sequence data alone.

Recycling eutrophic lake sediments into grass production: A four-year field experiment on agronomical and environmental implications.

Inefficient use of phosphorus (P) fertilizers leads to the transfer of P into water bodies, causing their eutrophication. Sediment removal is a promising lake restoration strategy that removes nutrients including P accumulated in lake sediments, and opens the opportunity to use removed nutrients in agriculture. In the present study, we investigated the effects of using a thick layer of sediment from the eutrophic Lake Mustijärv on plant growth, and estimated the environmental impacts of different sediment application methods by analyzing greenhouse gas emissions, N and P leaching, aggregate stability, and soil biota. The field experiment (2017-2020) was established on the lake shore with the following treatments: the agricultural control soil (Soil) surrounding the lake, pure sediment (Sed), biochar-treated sediment (SB), and biochar and soil mixed with sediment (SSB). The sediment-based treatments resulted in a similar grass growth performance to the Soil. The availability of most macro- and micronutrients including P (75 vs. 21 g m-3) were far greater in the Sed compared to the Soil. The sediment-based growing media emitted more CO2 than the Soil (579 vs. 400 mg CO2 - C m-2 h-1) presumably due to the high rate of organic matter decomposition. The bacterial and fungal community structures of the Sed were strongly differentiated from those of Soil. Also, Sed had lower bacterial diversity and a higher abundance of the bacterial phyla associated with solubilizing P including Proteobacteria and Chloroflexi. Sediment-based growing media increased more than seven times the risk of mineral N and P leaching, and the biochar treatment only had a short-lived beneficial effect on reduction of the sediment's leached P concentration. The sediment application rate should be adjusted to match the crop requirements to minimize greenhouse gas emissions and nutrient leaching when upscaling the case study to larger lakes with similar sediment properties.