Species Of Soil Bacteria Research Articles

Heterogeneous Habitats in Taiga Forests with Different Important Values of Constructive Species Changes Bacterial Beta Diversity.

As a crucial link between the aboveground and belowground components of forest ecosystems, soil bacterial communities are extremely sensitive to changes in plant communities and soil conditions. To investigate the impact of the difference of constructive species on soil bacterial communities in taiga forests, we conducted a vegetation survey at the international monitoring plot of the Larix gmelinii forests in the Great Khingan Mountains and calculated the important value of Larix gmelinii to determine experimental groups based on this survey. Subsequently, we collected soil samples for high-throughput sequencing to analyze how the soil bacterial community composition and diversity changed, and which factors affected them. The results showed that taiga forests with different important values of Larix gmelinii had heterogeneous habitats, in which the soil AP content significantly increased, and the SOC, MBC, pH, and C/N content decreased significantly (p < 0.05). A total of 32 phyla, 91 classes, 200 orders, 308 families, 496 genera, and 975 species of soil bacteria were obtained by sequencing. Among them, Proteobacteria, Actinobacteriota, and Acidobacteriota were the dominant phyla, and Mycobacterium was the dominant genus, and the relative abundance of each bacterial group was varied. The beta diversity of soil bacteria showed extremely significant differences (p = 0.001), with SOC, C/N, MBC, AP, TN, pH, AN, and WC being the main influencing factors. Functional prediction analysis showed that chemoheterotrophy and aerobic chemoheterotrophy were the main bacterial functional groups, and the relative abundance of each functional group was significantly different (p < 0.05). Overall, taiga forests with differences in constructive species had heterogeneous habitats, which changed the community composition, beta diversity, and potential functions of soil bacteria.

Effects of Combined Application of Fungal Residue and Chemical Fertilizer on Soil Microbial Community Composition and Diversity in Paddy Soil

Fungal residue is a unique abundant organic material undervalued in agricultural production. The application of chemical fertilizer combined with fungal residue can not only improve soil quality but also regulate the microbial community. However, it is unclear whether the response of soil bacteria and fungi to the combined application of fungal residue and chemical fertilizer is consistent. Therefore, a long-term positioning experiment in a rice field was conducted with a total of nine treatments. Chemical fertilizer (C) and fungal residue (F) were applied at 0, 50%, and 100% to evaluate 1 the change in soil fertility properties and microbial community structure and 2 the main driving factors of soil microbial diversity and species composition. The results showed that soil total nitrogen (TN) was highest after treatment C0F100 (55.56% higher than in the control), and the carbon to nitrogen ratio (C/N), total phosphorus (TP), dissolved organic carbon (DOC), and available phosphorus (AP) contents were highest after treatment with C100F100(26.18%, 26.46%, 17.13%, and 279.54% higher than in the control, respectively). The amounts of soil organic carbon (SOC), available nitrogen (AN), available potassium (AK), and pH were highest after treatment with C50F100 (85.57%, 41.61%, 29.33%, and 4.62% higher than in the control, respectively). Following the application of fungal residue with chemical fertilizer, there were significant changes in the α-diversity of bacteria and fungi in each treatment. Compared with that of the control (C0F0), different long-term applications of fungal residue with chemical fertilizer did not significantly change soil bacterial β-diversity but resulted in significant differences in fungal β-diversity, and the relative abundance of soil fungal Ascomycota and Sordariomycetes significantly decreased after the application of C50F100. The random forest prediction model indicated that AP and C/N were the main driving factors of bacterial and fungal α-diversity, respectively, and AN, pH, SOC, and DOC were the main driving factors of bacterial β-diversity, whereas AP and DOC were the main driving factors of fungal β-diversity. Correlation analysis suggested that the relative abundance of soil fungal Ascomycota and Sordariomycetes had a significantly negative correlation with SOC, TN, TP, AN, AP, AK, and C/N. PERMANOVA showed that variation in soil fertility properties, dominant species of soil bacteria at the phylum and class level, and dominant species of soil fungi at the phylum and class level were all best explained by fungal residue (46.35%, 18.47%, and 41.57%, respectively), and variation in bacterial diversity was best explained by fungal residue (23.84%) and to a lesser extent by the interaction between fungal residue and chemical fertilizer (9.90%). In contrast, the variation in fungal diversity was best explained by the interaction between fungal residue and chemical fertilizer (35.00%) and to a lesser extent by fungal residue (10.42%). In conclusion, the application of fungal residue has more advantages than chemical fertilizer in influencing soil fertility properties and microbial community structure changes.

Bacterial community structure and diversity in the rhizospheric soil of Robinia pseudoacacia and Juniperus sabina planted in iron tailings matrix.

Iron tailings matrix is deficient in nutrients, and phytoremediation is one of the effective methods to improve tailings nutrients. The response of phytoremediation to tailings microorganisms remains to be studied. The present study analyzed rhizospheric soil of two kinds of plants bacterial diversity and community structure and their relationship with soil environmental factors. The results indicate that the rhizospheric soil bacteria species of Robinia pseudoacacia and Juniperus sabina were not significantly different from that of bare tailings, but rhizospheric soil bacterial community compositions and abundance were significantly different from that of bare tailings. Canonical correlation analysis (CCA) showed that soil alkali-hydrolyzable nitrogen (AN), soil total nitrogen (TN), and soil organic matter (SOM) were the main environmental factors affecting bacterial community diversity. Spearman's correlation analysis showed that AN, TN, and SOM were significantly positively correlated with the relative abundance of Gemmatimonadetes and Nitrospirae, and were significantly negatively correlated with that of Firmicutes, Fusobacteria, and Bacteroidetes. FAPROTAX function prediction showed that the functional microbial communities of rhizospheric soil of the two plants were significantly different from those of bare tailings. Overall, the findings support an increase of microbial diversity, SOM, and nitrogen in rhizospheric soil of revegetated tailings compared to bare tailings. These results provide theoretical support for the development and application of phytoremediation in abandoned mines.

Environmental stress leads to genome streamlining in a widely distributed species of soil bacteria

Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.

Intraspecies variability of the 16S rRNA gene of the soil bacteria Acinetobacter lwoffii and Paenibacillus taichungensis

The functioning of well-studied key groups of soil microorganisms depends on the microbial ecosystem in which they function in interaction with species belonging to other ecological groups. An analysis of the composition of the soil microbiota, and the possibility of analyzing the number of representatives of specific species, remains an urgent task of soil microbiology. Such analysis could be performed using modern and expensive methods such as metagenomics and mass-spectrometry, but some questions could also be answered using real-time PCR. This well-known approach is rather cheap for massive analysis and is ready to present reproducible results for practical agricultural applications. Understanding the variability of the primary structure of 16S rRNA is key to the reliable identification of bacterial species and provides an opportunity to choose the optimal pathways for their detection by PCR. In this work, analysis of the sequences of 16S rRNA of two species of soil bacteria, Acinetobacter lwoffii and Paenibacillus taichungensis is carried out. The most variable and most conservative areas on the level of species are detected. It was proved that conventional variable and conservative areas of the gene have on average nearly the same level of variability on the intraspecies level.

The effect of monoculture and rotation planting on soil bacterial community structure at different elevation in Hubei

AbstractHighland vegetables play an important role in meeting the demand for fresh vegetables in summer and also increasing the income of farmers in upland areas of China. With the large‐scale and intensive development of vegetable planting in upland areas, many of the farmers have used vegetable–maize rotation instead of the traditional maize monoculture pattern. The bacterial community and diversity under different planting patterns and elevations were investigated using next‐generation sequencing and Biolog Ecoplate. The average well colour development (AWCD) was greater at low elevation and under the vegetable–maize rotation. There were 15 classified bacterial genera related to the elevation and planting patterns. The relative abundance of Aquicella was significantly affected by elevation and WPS‐1_genera_incertae_sedis by elevation and planting patterns (p &lt; .01). At the same time, the only genus that was significantly affected by planting patterns was Aquicella (p &lt; .05). Redundancy analysis (RDA) showed that soil pH and available N content were the main factors influencing the change in soil bacterial community structure in the different planting models and elevation, and the dominant species of soil bacteria were Streptophyta and Aridibacter.

Can Toxicities Induced by Insecticide Methomyl be Remediated Via Soil Bacteria Ochrobactrum thiophenivorans and Sphingomonas melonis?

The research study was about revealing the biochemical response of Gammarus pulex related to insecticide methomyl before and after bioremediation by two soil bacteria species, Ochrobactrum thiophenivorans and Sphingomonas melonis. Catalase (CAT), glutathione S-transferase.(GST), cytochrome. P4501A1 (CYP1A1) activities in G. Pulex related to methomyl solution were investigated in 24h and 96h. ELISA method was used for test studies. CAT enzyme was decreased in Gammarus pulex that was exposed to methomyl after all exposure period (P < 0.05). CAT activities were returned to control results after bioremediation assays. GST enzyme activity was decreased depending on methomyl exposure during 24h but increased during 4days (P < 0.05). After 8days of bioremediation period, GST activity increased again during 24h while decreased during 4days (P < 0.05). CYP1A1 activity increased in Gammarus pulex that was exposed to methomyl after all exposure period (P > 0.05). After bioremediation, statistically significant changes were not revealed in CYP1A1 activities (P > 0.05). According to the results of our study, CYP1A1, CAT, and GST activities in G. pulex sanctioned the capability of Ochrobactrum thiophenivorans and Sphingomonas melonis in methomyl bioremediation. Isolated and enriched Ochrobactrum thiophenivorans and Sphingomonas melonis that were added to 2.5ppb concentrations of methomyl for 8 days. Each day, chemical oxygen demand (COD) and biochemical oxygen demand (BOD5), pH and dissolved oxygen parameters were monitored. At the final phase of the bioremediation step, it was determined that these bacteria have efficient methomyl bioremediation properties in a mixed corsortia at a rate of 86%. These results show that these bacteria can be used for bioremediate the receiving environments that are polluted by these kinds of insecticides.

Effects of Different Land Use Typess on the Molecular Ecological Network of Soil Bacteria

The bacterial community composition in four land-use types was determined and the visualized bacterial network was constructed by 16S rDNA Illumina MiSeq high-throughput sequencing technology and a molecular ecological network method. The results show that Proteobacteria, Acidobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, Planctomycetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Firmicutes, Nitrospirae, and Chlorobi are the main bacteria in this area. The number of nodes of urban green land, paddy field, and dry field bacteria networks is higher, and that of natural forest land is lower. The number of connections and average connectivity of dry fields are the highest; following are those of urban green land and paddy field, and those of natural forest land are the lowest. The four bacterial networks are dominated by positive correlation, and the ratio of competition relationship is TL > LD > HT > ST. The average network path and modularity of the soil bacteria networks of paddy field and dry land are small, while the average connectivity and clustering coefficient are higher. Some flora of Acidobacteria, Firmicutes, and Proteobacteria play an important role in the soil bacterial network in this area. The classification of operational taxonomic units is different among the key nodes of different bacterial molecular ecological networks, and there is almost no overlap. The relative abundance of bacteria of some key nodes in the four bacterial networks is low (<1%), and these are not the main bacteria in this area. The soil microflora in dry land are mainly affected by TP (P<0.05), the soil microflora in paddy field were mainly affected by clay, silt, and water content (P<0.05), and that in natural forest land and urban green land were mainly affected by C/N (P<0.05). The above results show that different land-use patterns lead to changes in soil physical and chemical properties and the interaction between soil bacteria species. The bacterial network of dry land soil is larger and the relationship between species is more complex. The bacteria in different land-use types are mainly cooperative, and the competition is weak. Compared with other land-use types, there is stronger competition between the bacteria in natural forest soil. The soil bacteria in paddy field and dry land are the most sensitive to the external environment, respond more quickly, and the community structure is easier to change. The response of soil bacteria in natural forest land and urban green land is slower, and the disturbance of environmental factors does not affect the whole bacterial ecological network in a short time, and thus the community structure is more stable. Some bacteria have the phenomenon of species role transformation between networks. The abundance and community distribution of microorganisms cannot indicate the strength of their connectivity between network nodes; low-abundance bacteria in soil play an important role in the construction of bacterial networks.

The composition of phospholipid model bacterial membranes determines their endurance to secretory phospholipase A2 attack – The role of cardiolipin

Soil bacteria are decomposer organisms crucial for the biodegradation of organic pollutants, mineralization of dead organic matter and the turnover of biogenic elements. In their environment they are constantly exposed to membrane-lytic enzymes emitted to the soil by other microorganisms competing for the same niche. Therefore, the composition and structure of their membranes is of utmost importance for survival in the harsh environment. Although soil bacteria species can be Gram-negative or Gram-positive and their membranes differ significantly, they are formed by phospholipids belonging mainly to three classes: phosphatidylethanolamines (PE), phosphatidylglycerols (PG) and cardiolipins (CL). The correlation of the membrane phospholipid composition and its susceptibility to secretory membrane-lytic enzymes is widely unknown; thus, to shed light on these phenomena we applied the Langmuir monolayer technique to construct models of soil bacteria membranes differing in the mutual proportion of the main phospholipids. To characterize the systems we studied their elasticity, mesoscopic texture, 2D crystalline structure and discussed the thermodynamics of the interactions between their components. The model membranes were exposed to secretory phospholipase A2. It turned out that in spite of the structural similarities the model membranes differed significantly in their susceptibility to s-PLA2 attack. The membranes devoid of cardiolipin were completely degraded, whereas, these containing cardiolipin were much more resistant to the enzymatic hydrolysis. It also turned out that the sole presence of cardiolipin in the model membrane did not guarantee the membrane durability and that the interplay between cardiolipin and the zwitterionic phosphatidylethanolamine was here of crucial importance.

Effects of ectoine on animals and humans

Some species of soil bacteria and most organisms living in extreme environments such as salt lakes or coal or salt mines have effective protective mechanisms that enable them to function under adverse conditions. A common way to protect against harmful environmental factors is the production and accumulation of substances with an osmoprotective effect. One of such substances is ectoine, or 1,4,5,6-tetrahydro-2-methyl-4- -pyrimidine-carboxylic acid of an amphoteric nature. The effect of ectoin, mainly based on the binding of water molecules, has found wide application in the protection of macromolecules and cells. This work is a review of the use of this amino acid in human and veterinary medicine.

Effects of a vegetable-eel-earthworm integrated planting and breeding system on bacterial community structure in vegetable fields

Agricultural production combined with planting and breeding, which can reduce chemical fertilizer and pesticide applications, reduce losses due to natural disasters, and improve the output and quality of agricultural products, is an important way to achieve green, circular and efficient production. To assess effects on soil bacterial community structure, a vegetable-eel-earthworm integrated planting and breeding platform (VEE-IPBP) combined with experiment planting was established at Chongming Island, Shanghai and compared to traditional planting. High-throughput sequencing to reveal soil bacterial community structure was performed on samples collected at 0, 3 and 6 years after implementation of the two models. Over time, the Shannon index first increased and then decreased in the VEE-IPBP system and was reduced by 3.2% compared to the traditional planting (In the same time and space scale, the single-degree planting method of dryland vegetables under mechanical cultivation is adopted) (p < 0.05). In contrast, Chao and Ace indices were increased by 2.4% and 3.2%. Thus, soil bacterial diversity was markedly different in the two planting models. The abundance of Proteus, Cyanophyta and Cyanophyta in soil increased after 6 years, and the proportion of Lysinibacillus increased significantly, contributing to improvement in soil disease resistance. Redundancy analysis (RDA) showed that the soil pH and water content were the main factors influencing the change in soil bacterial community structure in the two planting models, and the dominant species of soil bacteria were Lysobacter and Bacillus.

Proposal of three novel species of soil bacteria, Variovorax ureilyticus, Variovorax rhizosphaerae, and Variovorax robiniae, in the family Comamonadaceae.

Three novel bacterial strains (UCM-2T, UCM-G28T, and UCM-G35T) were obtained while isolating soil bacteria for the development of antibiotics. Cells of these strains were Gram-negative, non-spore forming, motile by means of a single flagellum, and rod shaped. In all strains, the predominant isoprenoid quinone was ubiquinone-8 (Q-8). Cells contained C16:0, summed feature 3 (C16:1ω7c and/or C16:1ω6c), summed feature 8 (C18:1ω7c and/or C18:1ω6c), and C17:0 cyclo as the major fatty acids, and C10:0 3-OH as the major hydroxy fatty acid. The polar lipid profiles of the three novel strains were dominated by diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylglycerol. The genomic DNA G + C contents of strains UCM-2T, UCM-G28T, and UCMG35T were 67.5, 65.9, and 66.4 mol%, respectively. Phylogenetic analyses based on 16S rRNA sequences showed that strain UCM-2T was most closely related to Variovorax soli NBRC 106424T, whereas strains UCM-G28T and UCM-G35T were most similar to Variovorax ginsengisoli Gsoil 3165T. Values indicating DNA-DNA hybridization between the novel isolates and closely related species in the genus Variovorax were lower than the 70% cut-off point. These phenotypic, chemotaxonomic, and phylogenetic data indicate that the three isolates should be classified as new members of the genus Variovorax, for which the names Variovorax ureilyticus sp. nov., Variovorax rhizosphaerae sp. nov., and Variovorax robiniae sp. nov. are proposed. The type strains are UCM-2T (= KACC 18899T = NBRC 112306T), UCMG28T (= KACC 18900T = NBRC 112307T), and UCM-G35T (= KACC 18901T = NBRC 112308T), respectively.

The Catabolism of Nicotinic Acid and Nicotine and the Role of a Putative Monooxygenase in Bacillus niacini

N‐Heteroaromatic compounds (NHACs) comprise a class of molecules that are commonly found in pharmaceuticals, personal care products, and pesticides and are known to have toxic effects on the environment. Intriguingly, certain species of soil‐dwelling bacteria have the innate ability to degrade particular NHACs. A better understanding of how these soil bacteria degrade NHACs has important implications in the development of bioremediation techniques to remove toxic compounds from the environment. This investigation focuses on developing preexisting hypotheses in regards to how Bacillus niacini, a ubiquitous species of soil bacteria, degrades nicotinic acid (NA) and nicotine, both of which are NHACs. It has been hypothesized that the non‐canonical NA degradation pathway in B. niacini involves a reaction in which 2,6‐dihydroxynicotinic acid (2,6‐DHNA) undergoes oxidative decarboxylation to form 2,3,6‐trihydroxypyridine by an enzyme termed NicC‐like. Two methods have been utilized to establish the identity of the nicC‐like gene. First, a novel transformation technique was developed to generate a B. niacini knock out variant lacking the putative nicC gene. Second, the substrate for the NicC‐like enzyme, 2,6‐DHNA, was synthesized with a 60% yield. The substrate was utilized to assess the kinetic activity of the NicC‐like enzyme. Though there are hypotheses regarding the identity of the nicC‐like gene and its involvement in NA catabolism, sequence analysis indicates that the nicC‐like gene is only 21% similar to the nicC gene involved in NA degradation in Pseudomonas putida. In contrast, the nicC‐like gene is 24% similar to HspB, which encodes an enzyme involved in nicotine degradation. Additionally, the structure and the associated catabolic processes of nicotine and NA are similar, suggesting that the novel nicC‐like gene in B. niacini might play a role in either nicotine or NA degradation. Preliminary HPLC evidence indicates that B. niacini does not degrade nicotine. Furthermore, the NicC‐like enzyme is not kinetically active when incubated with the substrate of the HspB enzyme, 6‐Hydroxyl‐3‐succinoyl‐pyridine. Thus, the genes currently hypothesized to encode the enzymes necessary for NA catabolism do not code for nicotine degradation enzymes. Characterizing the reaction catalyzed by the putative NicC‐like enzyme and determining whether or not B. niacini catabolizes nicotine has led to an improved understanding about the genes necessary for NA degradation by this particular species of pervasive soil bacteria. Continued contributions to this field may eventually lead to the development of techniques to remove NHACs from the environment.Support or Funding InformationHenry J. Copeland Fund for Independent Study at the College of WoosterThis abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing.

The present study aimed to identify the structural succession of the bacteria community in soil during long-term continuous cotton cropping and its relationship with continuous cropping obstacles in Xinjiang, China. High-throughput sequencing was used to analyze and compare the composition of the bacterial community in the soil at the cotton root zone after years of continuous cotton cropping and crop rotation over 30years of cultivation. Cotton cultivation increased the structural diversity of the bacterial community, among which the populations of Actinobacteria, Acidobacteria, Firmicutes, Nitrospirae, and Chloroflexi changed considerably. A 0-year sample and samples after continuous short- and long-term cropping, along with some with crop rotation, were gathered into three individual clusters. The findings of the rotation sample were similar to those of the sample of continuous long-term cropping. Cropping is the main cause of changes in the structure of the bacteria community; however, the new structure formed under continued duress of both long-term cotton cultivation and the associated farming methods gradually stabilizes after 10years of repeated fluctuations. Crop rotation can lead to the rapid recovery of some species of soil bacteria.

Linearmycins Activate a Two-Component Signaling System Involved in Bacterial Competition and Biofilm Morphology.

Bacteria use two-component signaling systems to adapt and respond to their competitors and changing environments. For instance, competitor bacteria may produce antibiotics and other bioactive metabolites and sequester nutrients. To survive, some species of bacteria escape competition through antibiotic production, biofilm formation, or motility. Specialized metabolite production and biofilm formation are relatively well understood for bacterial species in isolation. How bacteria control these functions when competitors are present is not well studied. To address fundamental questions relating to the competitive mechanisms of different species, we have developed a model system using two species of soil bacteria, Bacillus subtilis and Streptomyces sp. strain Mg1. Using this model, we previously found that linearmycins produced by Streptomyces sp. strain Mg1 cause lysis of B. subtilis cells and degradation of colony matrix. We identified strains of B. subtilis with mutations in the two-component signaling system yfiJK operon that confer dual phenotypes of specific linearmycin resistance and biofilm morphology. We determined that expression of the ATP-binding cassette (ABC) transporter yfiLMN operon, particularly yfiM and yfiN, is necessary for biofilm morphology. Using transposon mutagenesis, we identified genes that are required for YfiLMN-mediated biofilm morphology, including several chaperones. Using transcriptional fusions, we found that YfiJ signaling is activated by linearmycins and other polyene metabolites. Finally, using a truncated YfiJ, we show that YfiJ requires its transmembrane domain to activate downstream signaling. Taken together, these results suggest coordinated dual antibiotic resistance and biofilm morphology by a single multifunctional ABC transporter promotes competitive fitness of B. subtilisIMPORTANCE DNA sequencing approaches have revealed hitherto unexplored diversity of bacterial species in a wide variety of environments that includes the gastrointestinal tract of animals and the rhizosphere of plants. Interactions between different species in bacterial communities have impacts on our health and industry. However, many approaches currently used to study whole bacterial communities do not resolve mechanistic details of interspecies interactions, including how bacteria sense and respond to their competitors. Using a competition model, we have uncovered dual functions for a previously uncharacterized two-component signaling system involved in specific antibiotic resistance and biofilm morphology. Insights gleaned from signaling within interspecies interaction models build a more complete understanding of gene functions important for bacterial communities and will enhance community-level analytical approaches.

Suppression of Enteric Bacteria by Bacteriophages: Importance of Phage Polyvalence in the Presence of Soil Bacteria.

Bacteriophages are widely recognized for their importance in microbial ecology and bacterial control. However, little is known about how phage polyvalence (i.e., broad host range) affects bacterial suppression and interspecies competition in environments harboring enteric pathogens and soil bacteria. Here we compare the efficacy of polyvalent phage PEf1 versus coliphage T4 in suppressing a model enteric bacterium (E. coli K-12) in mixtures with soil bacteria (Pseudomonas putida F1 and Bacillus subtilis 168). Although T4 was more effective than PEf1 in infecting E. coli K-12 in pure cultures, PEf1 was 20-fold more effective in suppressing E. coli under simulated multispecies biofilm conditions because polyvalence enhanced PEf1 propagation in P. putida. In contrast, soil bacteria do not propagate coliphages and hindered T4 diffusion through the biofilm. Similar tests were also conducted under planktonic conditions to discern how interspecies competition contributes to E. coli suppression without the confounding effects of restricted phage diffusion. Significant synergistic suppression was observed by the combined effects of phages plus competing bacteria. T4 was slightly more effective in suppressing E. coli in these planktonic mixed cultures, even though PEf1 reached higher concentrations by reproducing also in P. putida (7.2 ± 0.4 vs 6.0 ± 1.0 log10PFU/mL). Apparently, enhanced suppression by higher PEf1 propagation was offset by P. putida lysis, which decreased stress from interspecies competition relative to incubations with T4. In similar planktonic tests with more competing soil bacteria species, P. putida lysis was less critical in mitigating interspecies competition and PEf1 eliminated E. coli faster than T4 (36 vs 42 h). Overall, this study shows that polyvalent phages can propagate in soil bacteria and significantly enhance suppression of co-occurring enteric species.

Isolation, screening and identification of mercury resistant bacteria from mercury contaminated soil

New bacterial strains resistant to high concentration of mercury were obtained and character iz ed focusing on their potential application in bioremediation. The biological material was isolated from soil contaminated with mercury. The ability to removal of Hg from the liquid medium and the effect of the various pH and mercury concentrations in the environment on bacterial strains growth kinetics were tested. The selected strains were identified by analysis of the 16S ribosome subunit coding sequenc es as Pseudomonas syringae. The analysis of Hg concentration in liquid medium as effect of microbial metabolism demonstrated that P. syringae is able to remove almost entire metal from medium after 120 hours of incubation. Obtained results revealed new ability of the isolated strain P. syringae. Analyzed properties of this soil bacteria species able to reduce concentration of Hg ors immobi lize this metal are promising for industrial wastewater treatment and bioremediation of the soils polluted especially by mercury lamps scrapping, measuring instruments, dry batteries, detonators or burning fuels made from crude oil, which may also contain mercury. Selected bacteria strains provide efficient and relatively low-cost bioremediation of the areas and waters contaminated with Hg.

Interactions of three soil bacteria species with phyllosilicate surfaces in hybrid silica gels

To simulate iron consumption in soils, iron leaching from silicate minerals due to three heterotrophic bacterial strains and a chemical treatment was studied using hybrid silica gel (HSG) doped with two phyllosilicates, nontronite (NAu-2) or low-iron-content montmorillonite (SWy-2). HSG methodology, a novel way of separating bacteria cells from a colloidal mineral source, consisted in embedding colloidal mineral particles into an amorphous porous silica matrix using a classical sol-gel procedure. Pantoae agglomerans PA1 and Rahnella aquatilis RA1 were isolated from silicate-rich soils, that is, beech and wheat rhizospheres (Vosges, France); Burkholderia sp. G5 was selected from acidic and nutrient-poor podzol soils (Vosges, France). Fe release from clay minerals and production of bacterial metabolites, that is, low molecular weight organic acids (LMWOA) and siderophores, were monitored. Two LMWOA profiles were observed with major gluconate production (>9000μM) for Burkholderia sp. G5 and moderate production of lactate, acetate, propionate, formate, oxalate, citrate, and succinate (<300μM) for R.aquatilis RA1 and P.agglomerans PA1. HSG demonstrated its usefulness in revealing clay mineral-microorganisms interactions. The effect of bacterial exsudates was clearly separated from physical contact effect.

杉木人工林土壤质量演变过程中土壤微生物群落结构变化

Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis(PCR-DGGE),DNA-sequencing,and Principal Component Analysis(PCA) technologies were adopted to assess the soil microbial community structure changes during the evolution of Cunninghamia lanceolata plantation soil quality.The relationship between soil microbial community structure and soil quality changes was analyzed from C.Lanceolata plantations with different soil qualities at the Huitong Experimental Station of Forest Ecology,CAS.The dominant species of soil bacteria in the C.Lanceolata plantations in this region are α,β,γ-proteobacteria,and Cytophaga Flexibacter Bacterioides(CFB).The dominant species of fungi are the Ascomycetes and Basidiomycetes subphylum species.The Shannon index showed that bacterial diversity associated with monospecific C.lanceolata plantations was lower than that of the natural forest or mixed C.lanceolata plantations.With continuous planting of artificial fir,the index continues to decrease.The replacement of natural forest with artificial fir also affects microbial species composition.For example,bacteria species with a close phylogenetic relationship to Pedobacter cryoconitis disappear from the artificial fir plantation soil.However,bacteria species with a close phylogenetic relationship to Xanthomonas sp.and Rhodanobacter sp.begin to appear in the soil of the continuously planted artificial fir forest.The pattern of change in the fungi community structure is opposite to that in the bacteria community.When the artificial fir forest replaces the natural forest,artificial fir is continuously planted,and the soil fungi diversification index continues to increase.The fungi community structure varies significantly between the third generation of artificial fir forest and the natural forest.Some fungi became dominant in the third generation of artificial fir forest,including Sclerotinia sclerotiorum,Mycosphaerella cannabis and Marasmius graminum.Other research has shown that S.sclerotiorum and M.cannabis can cause a variety of plant diseases,and M.graminum is a litter decomposition bacterium.The dominant fungi species originally existing in the natural forest soil disappear from the third generation artificial fir forest soil.The soil bacteria and fungi community structures of the mixed C.lanceolata-Michelia macclurei and C.lanceolata-Alnus cremastogyne plantations are similar to the dominant edaphon species in the natural forest.This study evaluated the relationship between soil quality evolution and changes in microbial communities and functional groups by correlation analysis.The soil bacteria diversification index has a positive correlation with the total organic carbon(TOC),total nitrogen(TN),extracted Carbon(Cext),ammoniacal nitrogen(NH+4-N),available potassium,available phosphorus and pH of the soil.The fungi diversification index change is positively correlated with the C ∶N ratio in the soil but negatively correlated with the pH.These findings suggest that different silvicultural practices have significant impacts on the soil microbial community through influences on soil chemical properties.There were significant correlations between soil quality evolution and changes in dominant soil microorganism species and soil quality change is related to the dominant species changes in soil bacteria and fungi.For example,Burkholderia sp.and Pedobacter sp.can dissolve phosphorus and potassium and the pathogenic bacteria Xanthomonas sp.,and pathogenic fungi S.sclerotiorum and M.cannabis can cause plant diseases.The dominance of these species changes with soil quality evolution from natural forest to artificial fir plantations.

Influence of inoculation with plant growth promoting rhizobacteria (PGPR) on tomato plant growth and nematode reproduction under greenhouse conditions

Numerous species of soil bacteria which flourish in the rhizosphere of plants or around plant tissues stimulate plant growth and reduce nematode population by antagonistic behavior. These bacteria are collectively known as PGPR (plant growth promoting rhizobacteria). The effects of six isolates of PGPR Pseudomonas putida, Pseudomonas fluorescens, Serratia marcescens, Bacillus amyloliquefaciens, Bacillus subtilis and Bacillus cereus, were studied on tomato plant growth and root knot nematode reproduction after 45days from nematode infection. The highest number of shoot dry weight/g (43.00g) was detected in the plant treated with S. marcescens; then P. putida (34.33g), B. amyloliquefaciens (31.66g), P. fluorescens (30.0g), B. subtilis (29.0g), B. cereus (27.0g) and nematode alone (untreated) 20g/plant. While the highest number of plant height was observed when plant was treated with S. marcescens, P. fluorescens, P. putida, B. amyloliquefaciens and P. putida 52.66, 50.66, 48 and 48cm respectively. No significant differences were seen between previous treatments but only had significant differences compared with untreated plant. The highest number of fruit/plant was observed when plants were treated with S. marcescens (10.66), then B. amyloliquefaciens (8.66), P. putida (8), P. fluorescens (8) and B. cereus (7.66). No significant differences between the last 4 treatments, but all had significant differences compared with untreated plants. The highest weight of plant yield (g) was observed with S. marcescens (319.6g/plant) and the lowest weight of plant yield was observed in plants treated with nematode alone (untreated). On the other hand, the lowest numbers of J2/10g of soil (78), galls/root, (24.33) galls/root, egg masses/root (12.66) and egg/egg masses were observed in the plants treated with S. marcescens.