Culturable Bacterial Community Research Articles

Census of cultivable bacterial community in common effluent treatment plant (CETP) of tannery discharge and computational scrutiny on their leading residents

Common effluent treatment plant (CETP) for tannery effluent, is the combination of physical, chemical and biological treatment to facilitate the degradation of industrial waste water. Obviously, the biomass which survives in this extreme environment may have the ability to utilize the effluent as the sole carbon source for its survival. The ultimate aim of the present investigation is to expose the microbial diversity in each stage of the CETP through the culture dependent way. Bacterial diversity in the effluent were analysed through 16S rRNA gene. The community study revealed the dominance of firmicutes and the dominant genus was Bacillus sp, with variable species diversity. Notably, Putative Bacillus sp, B. firmus and B. licheniformis were observed in all stages of treatment. The dominant residents were analysed by BProm and TF site scan to prove their uniqueness. This species richness indicates the capability of liveliness in treatment plant and whose can be exploited for treating the effluent by using modern molecular approach.AbbreviationsCETP - Common Effluent Treatment Plant, PTIET - Pallavaram Tanners Industrial Effluent Treatment Company Ltd.

Diversity and Chemical Defense Role of Culturable Non-Actinobacterial Bacteria Isolated from the South China Sea Gorgonians

The diversity of culturable non-actinobacterial (NA) bacteria associated with four species of South China Sea gorgonians was investigated using culture-dependent methods followed by analysis of the bacterial 16S rDNA sequence. A total of 76 bacterial isolates were recovered and identified, which belonged to 21 species of 7 genera, and Bacillus was the most diverse genus. Fifty-one percent of the 76 isolates displayed antibacterial activities, and most of them belonged to the Bacillus genus. From the culture broth of gorgonian-associated Bacillus methylotrophicus SCSGAB0092 isolated from gorgonian Melitodes squamata, 11 antimicrobial lipopeptides including seven surfactins and four iturins were obtained. These results imply that Bacillus strains associated with gorgonians play roles in coral defense mechanisms through producing antimicrobial substances. This study, for the first time, compares the diversity of culturable NA bacterial communities among four species of South China Sea gorgonians and investigates the secondary metabolites of gorgonian-associated B. methylotrophicus SCSGAB0092.

주황해변해면(Hymeniacidon sinapium) 공생세균 군집의 계절적 차이

Seasonal differences of the cultivable bacterial communities associated with the marine sponge, Hymeniacidon sinapium, between spring and summer were analyzed through the Amplified Ribosomal DNA Restriction Analysis (ARDRA). For the cultivation of the bacterial isolates, modified Zobell and MA media were used. The 16S rDNA of individual strains were amplified and fragmented by using two restriction enzymes, HaeIII and MspI. As a result, 23 ARDRA types from the spring sponge and 28 types from the summer sponge were obtained. The partial sequencing result of 1 to 3 selected strains from each types showed over 94% similarities with the known species from the public database. The bacterial communities from the sponge, captured on spring, contained 4 phyla: Actinobacteria, Alphaproteobacteria, Gammaproteobacteria, and Firmicutes. There were 5 phyla observed from the bacterial communities associated with the sponge, captured on summer: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Firmicutes, and Bacteroidetes. Gammaproteobacteria was predominant group in both spring and summer, accounted for 33.8% of total in spring and 67.4% in summer, showed increase pattern on summer. Because Firmicutes and Actinobacteria participated in 30.2% and 8.3% of the spring sponge while they represented only 6.9% and 0% of the summer sponge, both bacterial groups showed decrease drift on summer. Betaproteobacteria (4.7%) and Bacteroidetes (4.7%) were only observed on the sponge captured on summer. On the sponge, Hymeniacidon sinapium, more diverse bacterial communities were shown on summer than on spring, and even from the same sponge, there were seasonal differences.

Local Environmental Pollution Strongly Influences Culturable Bacterial Aerosols at an Urban Aquatic Superfund Site

In polluted environments, when microbial aerosols originate locally, species composition of the aerosols should reflect the polluted source. To test the connection between local environmental pollution and microbial aerosols near an urban waterfront, we characterized bacterial aerosols at Newtown Creek (NTC), a public waterway and Superfund site in a densely populated area of New York, NY, USA. Culturable bacterial aerosol fallout rate and surface water bacterial concentrations were at least an order of magnitude greater at NTC than at a neighboring, less polluted waterfront and a nonurban coastal site in Maine. The NTC culturable bacterial aerosol community was significantly different in taxonomic structure from previous urban and coastal aerosol studies, particularly in relative abundances of Actinobacteria and Proteobacteria. Twenty-four percent of the operational taxonomic units in the NTC overall (air + water) bacterial isolate library were most similar to bacterial 16S rRNA gene sequences previously described in terrestrial or aquatic environments contaminated with sewage, hydrocarbons, heavy metals, and other industrial waste. This study is the first to examine the community composition and local deposition of bacterial aerosols from an aquatic Superfund site. The findings have important implications for the use of aeration remediation in polluted aquatic environments and suggest a novel pathway of microbial exposure in densely populated urban communities containing contaminated soil and water.

Characterization of culturable bacterial endophytes of switchgrass (Panicum virgatum L.) and their capacity to influence plant growth

AbstractSwitchgrass (Panicum virgatum L.) is a perennial warm season grass that is native to the plains of North America and is widely grown as a forage, bioenergy or groundcover crop. Despite its importance, a bottleneck in switchgrass production is poor seedling vigor, which as a perennial crop represents an important time for management. Herein, data identify a suite of culturable bacterial microflora extracted from switchgrass, and show their capability to influence host plant growth and development. A total of 307 bacterial isolates were cultured and isolated from surface sterilized switchgrass biomass and sequence identified into 76 strains (subspecies classification), 36 species and 5 phyla. Approximately 58% of bacterial strains, when reintroduced into surface‐sterilized switchgrass seeds, were documented to increase lamina length (cm from base to tip after 60 days growth) relative to uninoculated controls. Ecologically, Phylum Firmicutes was the most abundant bacterial classification and encompassed 75% of all isolates. Although the culturable bacterial community studies herein represent an unknown and assumedly minor proportion of the total microbiome, by focusing on culturable bacteria, we delineate functional feedback between the presence of isolated bacteria and switchgrass seedling growth.

Impact of salinity-tolerant MCM6 transgenic tobacco on soil enzymatic activities and the functional diversity of rhizosphere microbial communities

The development of genetically modified plants for agriculture has provided numerous economic benefits, but has also raised concern over the potential impact of transgenic plants upon the environment. The rhizosphere is the soil compartment that is directly under the influence of living roots; it constitutes a complex niche likely to be exploited by a wide variety of bacteria potentially influenced by the introduction of transgenes in genetically modified plants. In the present study, the impact of overexpression of the salinity stress-tolerant minichromosome maintenance complex subunit 6 (MCM6) gene upon functional diversity and soil enzymatic activity in the rhizosphere of transgenic tobacco in the presence and absence of salt stress was examined. The diversity of culturable bacterial communities and soil enzymes, namely, dehydrogenases and acid phosphatases, was assessed and revealed no significant (or only minor) alterations due to transgenes in the rhizosphere soil of tobacco plants. Patterns in principal components analysis showed clustering of transgenic and non-transgenic tobacco plants according to the fingerprint of their associated bacterial communities. However, the presence of MCM6 tobacco did not cause changes in microbial populations, soil enzymatic activities or the functional diversity of the rhizosphere soil microbial community.

Analysis and characterization of cultivable extremophilic hydrolytic bacterial community in heavy-metal-contaminated soils from the Atacama Desert and their biotechnological potentials

To isolate and characterize the cultivable community of hydrolase producers (amylase, protease, lipase, DNase, xylanase and pullulanase) inhabiting heavy-metal-contaminated soils in extreme conditions from the Atacama Desert. A total of 25 bacterial strains showing hydrolytic activities have been selected including halotolerants, extremely halotolerants and moderate halophiles. Most hydrolase producers were assigned to the family B acillaceae, belonging to the genera Bacillus (nine strains), Halobacillus (seven strains) and Thalassobacillus (five strains) and four isolates were related to members of the families Pseudomonadaceae, Halomonadaceae and Staphylococcaceae. The selected strains were then characterized for their tolerance pattern to six heavy metals, measured as minimal inhibitory concentrations (MICs). The diversity found in the cultivable bacterial community analysed is more limited than that detected in other ecological studies owing to the restrictive conditions used in the screening. The dominant bacteria were Firmicutes and particularly, species related to the genus Bacillus. This study is focused on the characterization of extremophilic hydrolytic bacteria, providing candidates as a source of novel enzymes with biotechnological applications.

Arbuscular mycorrhizal fungi and soil microbial communities under contrasting fertilization of three medicinal plants

The effects on soil microorganisms of a three-year cultivation programme using mineral and manure fertilization on three perennial medicinal plant species, lemon balm (Melissa officinalis L.), sage (Salvia officinalis L.), and lavender (Lavandula angustifolia Mill.), were studied. Root endophyte colonization, namely arbuscular mycorrhizal fungi (AMF), dark septate endophytes (DSE) and Olpidium spp., as well as AMF species richness and abundance in the soil, soil respiration, microbial biomass, and the activity and functional richness of culturable bacterial communities were assessed. In the mineral fertilization treatment (MRL), phosphorus and potassium fertilizers were incorporated at the beginning of the experiment, while nitrogen fertilizer was applied throughout its course. In the manure fertilization treatment (MAN), animal manure was applied once four years prior to soil and plant sampling. The soil under MRL was characterized by a higher pH and P, N and Ca contents. AMF colonization of sage under MAN was lower in comparison to MRL; however, no significant differences were found in the case of lemon balm and lavender. The results of the Plantago lanceolata L. laboratory bioassay in respect of the infectivity potential of the AMF present in the soils tested were in accordance with the trends obtained from mycorrhizal colonization assessments of the medicinal plant species. DSE and Olpidium spp. were also observed in the roots subjected to analysis; however, they were not abundant. In the case of sage, DSE were more frequent in MAN, while no significant differences were found in lemon balm and lavender. In contrast, Olpidium spp. were more abundant in the sage and lavender from MRL. Moreover, the lemon balm roots were devoid of these endophytes. The spores of 15 AMF species from 10 genera were isolated from trap cultures established from the soils collected in the field. The species richness found in MRL was higher than that in MAN. Moreover, four AMF species were detected exclusively in the trap cultures established from the soils collected from under lemon balm, two were exclusive to sage and one to lavender. The soil basal respiration was significantly affected by the plant species, but not by the fertilization systems and this parameter was lowest under lemon balm and highest under lavender. The microbial biomass differed significantly between management types only for lemon balm and was lower in MAN than in MRL. Bacterial activity was affected neither by plant species nor by fertilization type. Bacterial functional richness was significantly influenced only by the fertilization type in interaction with the plant species and was higher in MAN than in MRL for sage. Our results suggest that moderate application of mineral fertilizers does not suppress, and sometimes enhances, AMF and other soil microorganisms. Moreover, the effects of the fertilization type on soil microbial properties depend on the plant species being cultivated.

Ecotoxicological effects of decabromodiphenyl ether and cadmium contamination on soil microbes and enzymes

The ecotoxicological effects of decabromodiphenyl ether (BDE209) and cadmium (Cd) contamination on soil culturable microbial population, enzyme activity and bacterial community structure were investigated. Results of the indoor incubation test runs performed on many series of control and contaminated soil samples have demonstrated some notable toxic effects due to long term exposure to either or both contaminants. The two contaminants produced notable yet different toxic effects on the test microbes; the population of the exposed species generally declined according to certain dose–response relationships. The soil culturable microbial population and enzyme activity data show that the sensitivity to one or both contaminants followed the order of: bacteria>fungi>actinomycete and urease>saccharase, respectively. The interaction between BDE209 and Cd was dependent on both the exposure dose and time and that the joint toxic effects were synergistic, antagonistic or additive. The PCR-DGGE analysis data of species composition and richness suggest the synergistic combined effects on bacterial community structure during the 30d exposure. Pseudomonas tuomuerensis strain CCM 7280 and Pseudomonas alcaliphila strain AL15-21 were enriched, indicating these species might be major functional populations and highly tolerant. Such observations have provided the useful information of potential ecotoxicological effects of BDE209 and Cd contamination in the environment.

Plant Growth-Promoting Rhizobacteria Associated with Ancient Clones of Creosote Bush (Larrea tridentata)

Plant growth-promoting rhizobacteria (PGPR) are common components of the rhizosphere, but their role in adaptation of plants to extreme environments is not yet understood. Here, we examined rhizobacteria associated with ancient clones of Larrea tridentata in the Mohave desert, including the 11,700-year-old King Clone, which is oldest known specimen of this species. Analysis of unculturable and culturable bacterial community by PCR-DGGE revealed taxa that have previously been described on agricultural plants. These taxa included species of Proteobacteria, Bacteroidetes, and Firmicutes that commonly carry traits associated with plant growth promotion, including genes encoding aminocyclopropane carboxylate deaminase and β-propeller phytase. The PGPR activities of three representative isolates from L. tridentata were further confirmed using cucumber plants to screen for plant growth promotion. This study provides an intriguing first view of the mutualistic bacteria that are associated with some of the world's oldest living plants and suggests that PGPR likely contribute to the adaptation of L. tridentata and other plant species to harsh environmental conditions in desert habitats.

Variations in soil culturable bacteria communities and biochemical characteristics in the Dongkemadi glacier forefield along a chronosequence

The variations in the soil culturable bacterial communities and biochemical parameters of early successional soils from a receding glacier in the Tanggula Mountain were investigated. We examined low organic carbon (C) and nitrogen (N) contents and enzymatic activity, correlated with fewer bacterial groups and numbers in the glacier forefield soils. The soil pH values decreased, but the soil water content, organic C and total N significantly increased, along the chronosequence. The soil C/N ratio decreased in the early development soils and increased in the late development soils and it did not correlate with the soil age since deglaciation. The activities of soil urease, sucrase, protease, polyphenol oxidase, catalase, and dehydrogenase increased along the chronosequence. The numbers of culturable bacteria in the soils increased as cultured at 25°C while decreased at 4°C from younger soils to older soils. Total numbers of culturable bacteria in the soils cultured at 25°C were significantly positively correlated to the soil total N, organic C, and soil water content, as well as the activities of soil urease, sucrase, dehydrogenase, catalase, and polyphenol oxidase. We have obtained 224 isolates from the glacier forefield soils. The isolates were clustered into 28 groups by amplified ribosomal DNA restriction analysis (ARDRA). Among them, 27 groups and 25 groups were obtained from the soils at 25°C and at 4°C incubation temperatures, respectively. These groups are affiliated with 18 genera that belong to six taxa, viz, Actinobacteria, Gammaproteobacteria, Bacteroidetes, Firmicutes, Alphaproteobacteria, and Betaproteobacteria. The dominant taxa were Actinobacteria, Gammaproteobacteria, and Bacteroidetes in all the samples. The abundance and the diversity of the genera isolated at 25°C incubation temperature were greater than that at 4°C.

The culturable bacterial community of frass produced by larvae of Rhynchophorus ferrugineus Olivier (Coleoptera: Curculionidae) in the Canary island date palm

Larvae of the red palm weevil (RPW) Rhynchophorus ferrugineus Olivier (Coleoptera: Curculionidae) feed inside palm stem tissues, making galleries and producing a wet fermenting frass. We characterized the culturable bacteria associated with frass produced by tunnelling larvae inside the Canary island date palms and investigated the role of frass and gut bacteria in plant polymers breakdown. A culture-dependent method was used to isolate bacteria from frass and noninfested palm tissues. Bacterial isolates were grouped into operational taxonomic units based on polymorphisms in the ITS-PCR profiles, and representative isolates were identified by partial sequencing of the 16S rRNA gene. Frass bacteria were dominated by 2,3-butanediol fermenter Enterobacteriaceae. None of the bacterial isolates was able to degrade cellulose; however, cellulolytic and hemicellulolytic bacteria were isolated from the larval gut enrichment cultures. Frass bacteria are specifically associated with the RPW larvae and might play beneficial roles for RPW, other than nutritional, that deserve further investigations. Breakdown of plant polymers probably occurs inside the larvae digestive system. Frass and gut micro-organisms of R. ferrugineus should be included in studies of the interactions between RPW, its plant hosts, and its enemies.

Isolation and identification of diazotrophic bacteria from internal tissues ofPinus contortaandThuja plicata

Lodgepole pine ( Pinus contorta var. latifolia Engelm. ex S. Watson) and western red cedar ( Thuja plicata Donn ex D. Don) are capable of growing in soils that are severely nitrogen-limited. A rarely evaluated but possible nitrogen source for gymnosperms growing at nutrient poor sites is nitrogen fixation by endophytic bacteria. To investigate this possibility, we looked for nitrogen-fixing bacteria in surface-sterilized needle, stem, and root tissues of naturally regenerating lodgepole pine and western red cedar seedlings (2–4 years old) and trees (>20 years old) growing near Williams Lake, Chilliwack Lake, and Boston Bar, British Columbia, Canada. Ninety-nine bacterial isolates were obtained by plating surface-sterilized plant tissue extracts on tryptic soy agar (TSA) and combined carbon medium agar (CCMA), a nitrogen-free medium. Bacterial isolates were identified using gas chromatographic fatty acid methyl ester (GC-FAME) and 16S rRNA gene analyses and were evaluated for nitrogenase activity using an acetylene reduction assay. Representatives of the genera Bacillus and Paenibacillus dominated the culturable endophytic bacterial community in tissues of both tree species, with three Paenibacillus isolates and one Dyadobacter fermentans strain demonstrating consistently high acetylene-reduction activities. Our results raise the possibility that endophytic nitrogen fixation provides a supplementary nitrogen source for naturally regenerated lodgepole pine and western red cedar.

Causative Agents of White Band Disease From Culturable Bacterial Community Associated with Healthy and Diseased Corals Acropora humilis and Acropora tortuosa from Karimunjawa Islands, Indonesia

Causative Agents of White Band Disease From Culturable Bacterial Community Associated with Healthy and Diseased Corals Acropora humilis and Acropora tortuosa from Karimunjawa Islands, Indonesia

Comparison of microbial community structures in four Black soils along a climatic gradient in northeast China

Mi, L., Wang, G., Jin, J., Sui, Y., Liu, J. and Liu, X. 2012. Comparison of microbial community structures in four Black soils along a climatic gradient in northeast China. Can. J. Soil Sci. 92: 543–549. Surveys of microorganisms across climatic gradients provide important information about their biodiversity and spatial distribution, which is linked to fundamental ecological functions. The present study investigated the bacterial communities, including total and culturable communities, and fungal communities in Black soils collected from Lishu (lat. 43°20′N, long. 124°28′E), Dehui (lat. 44°12′N, long. 125°33′E), Hailun (lat. 47°26′N, long. 126°38′E) and Beian (lat. 48°17′N, long. 127°15′E) in northeast China. Bacterial and fungal communities were evaluated by polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) banding patterns of partial 16S rDNA and fungal rDNA internal transcribed spacer regions (ITS), respectively. Bacterial and fungal diversity, based on the number of DGGE bands, were similar among the locations, but cluster analysis of banding patterns showed distinct microbial communities along the climatic gradient. A closer relationship was found among soil bacterial (total and culturable) and fungal communities in neighboring locations than those at greater distance, which suggested that the spatial distribution of microbial community existed in the Black Soil Zone. Comparison of DGGE profiles among the four locations showed that the changes of fungal community and culturable bacterial community were greater than that of bacterial community, suggesting that fungal community and culturable bacterial community are more suitable to study microbial biogeographic distribution in Black soils.

Metabolism of DMSP, DMS and DMSO by the cultivable bacterial community associated with the DMSP-producing dinoflagellate Scrippsiella trochoidea

Bacterial species associated with the dimethylsulfoniopropionate (DMSP)-producing phytoplankton Scrippsiella trochoidea were cultured and identified, with the aim of establishing their ability to metabolise DMSP, dimethylsulfide (DMS) and dimethylsulfoxide (DMSO). Results demonstrate that of the cultivable bacteria only α-Proteobacteria were capable of producing DMS from DMSP. The concentration of DMSP was shown to affect the amount of DMS produced. Lower DMSP concentrations (1.5 μmol dm−3) were completely assimilated, whereas higher concentrations (10 μmol dm−3) resulted in increasing amounts of DMS being produced. By contrast to the restricted set of bacteria that metabolised DMSP, ~ 70% of the bacterial isolates were able to ‘consume’ DMS. However, 98-100% of the DMS removed was accounted for as DMSO. Notably, a number of these bacteria would only oxidise DMS in the presence of glucose, including members of the γ-Proteobacteria and Bacteroidetes. The observations from this study, coupled with published field data, identify DMS oxidation to DMSO as a major transformation pathway for DMS, and we speculate that the fate of DMS and DMSP in the field are tightly coupled to the available carbon produced by phytoplankton.

Phenotypic characterization and 16S rDNA identification of culturable non-obligate halophilic bacterial communities from a hypersaline lake, La Sal del Rey, in extreme South Texas (USA)

BackgroundLa Sal del Rey ("the King's Salt") is one of several naturally-occurring salt lakes in Hidalgo County, Texas and is part of the Lower Rio Grande Valley National Wildlife Refuge. The research objective was to isolate and characterize halophilic microorganisms from La Sal del Rey. Water samples were collected from the lake and a small creek that feeds into the lake. Soil samples were collected from land adjacent to the water sample locations. Sample salinity was determined using a refractometer. Samples were diluted and cultured on a synthetic saline medium to grow halophilic bacteria. The density of halophiles was estimated by viable plate counts. A collection of isolates was selected, gram-stained, tested for catalase, and characterized using API 20E® test strips. Isolates were putatively identified by sequencing the 16S rDNA. Carbon source utilization by the microbial community from each sample site was examined using EcoPlate™ assays and the carbon utilization total activity of the community was determined.ResultsResults showed that salinity ranged from 4 parts per thousand (ppt) at the lake water source to 420 ppt in water samples taken just along the lake shore. The density of halophilic bacteria in water samples ranged from 1.2 × 102 - 5.2 × 103 colony forming units per ml (cfu ml-1) whereas the density in soil samples ranged from 4.0 × 105 - 2.5 × 106 colony forming units per gram (cfu g-1). In general, as salinity increased the density of the bacterial community decreased. Microbial communities from water and soil samples were able to utilize 12 - 31 carbon substrates. The greatest number of substrates utilized was by water-borne communities compared to soil-based communities, especially at lower salinities. The majority of bacteria isolated were gram-negative, catalase-positive, rods. Biochemical profiles constructed from API 20E® test strips showed that bacterial isolates from low-salinity water samples (4 ppt) showed the greatest phenotypic diversity with regards to the types and number of positive tests from the strip. Isolates taken from water samples at the highest salinity (420 ppt) tended to be less diverse and have only a limited number of positive tests. Sequencing of 16S DNA displayed the presence of members of bacterial genera Bacillus, Halomonas, Pseudomonas, Exiguobacterium and others. The genus Bacillus was most commonly identified. None of the isolates were members of the Archaea probably due to dilution of salts in the samples.ConclusionsThe La Sal del Rey ecosystem supports a robust and diverse bacterial community despite the high salinity of the lake and soil. However, salinity does appear to a limiting factor with regards to the density and diversity of the bacterial communities that inhabit the lake and surrounding area.

Alteration of bacterial communities and organic matter in microbial fuel cells (MFCs) supplied with soil and organic fertilizer

The alteration of the organic matter (OM) and the composition of bacterial community in microbial fuel cells (MFCs) supplied with soil (S) and a composted organic fertilizer (A) was examined at the beginning and at the end of 3 weeks of incubation under current-producing as well as no-current-producing conditions. Denaturing gradient gel electrophoresis revealed a significant alteration of the microbial community structure in MFCs generating electricity as compared with no-current-producing MFCs. The genetic diversity of cultivable bacterial communities was assessed by random amplified polymorphic DNA (RAPD) analysis of 106 bacterial isolates obtained by using both generic and elective media. Sequencing of the 16S rRNA genes of the more representative RAPD groups indicated that over 50.4% of the isolates from MFCs fed with S were Proteobacteria, 25.1% Firmicutes, and 24.5% Actinobacteria, whereas in MFCs supplied with A 100% of the dominant species belonged to γ-Proteobacteria. The chemical analysis performed by fractioning the OM and using thermal analysis showed that the amount of total organic carbon contained in the soluble phase of the electrochemically active chambers significantly decreased as compared to the no-current-producing systems, whereas the OM of the solid phase became more humified and aromatic along with electricity generation, suggesting a significant stimulation of a humification process of the OM. These findings demonstrated that electroactive bacteria are commonly present in aerobic organic substrates such as soil or a fertilizer and that MFCs could represent a powerful tool for exploring the mineralization and humification processes of the soil OM.

Microbial diversity determines the invasion of soil by a bacterial pathogen.

Natural ecosystems show variable resistance to invasion by alien species, and this resistance can relate to the species diversity in the system. In soil, microorganisms are key components that determine life support functions, but the functional redundancy in the microbiota of most soils has long been thought to overwhelm microbial diversity-function relationships. We here show an inverse relationship between soil microbial diversity and survival of the invading species Escherichia coli O157:H7, assessed by using the marked derivative strain T. The invader's fate in soil was determined in the presence of (i) differentially constructed culturable bacterial communities, and (ii) microbial communities established using a dilution-to-extinction approach. Both approaches revealed a negative correlation between the diversity of the soil microbiota and survival of the invader. The relationship could be explained by a decrease in the competitive ability of the invader in species-rich vs. species-poor bacterial communities, reflected in the amount of resources used and the rate of their consumption. Soil microbial diversity is a key factor that controls the extent to which bacterial invaders can establish.

Tree girdling effect on bacterial substrate utilization pattern depending on stand age and soil microclimate in Eucalyptus plantations

It has been increasingly recognized that soil microorganisms and plants are tightly linked, however, the effects of belowground plant-carbon allocation on soil microbial communities has not been fully understood, particularly in subtropical and tropical forest ecosystems. In the present study, we conducted a tree-girdling experiment to explore the relationships between plant belowground carbon allocation and the functional diversity of soil microbial communities in two subtropical Eucalyptus plantations (2-year-old and 24-year-old). The functional diversity of soil culturable bacterial communities was characterized with community level physiological profile (CLPP) 1 year after tree girdling. We found that carbon substrate utilization patterns of soil culturable bacterial communities were significantly affected by both tree girdling and sampling season; but microbial metabolic activity and functional diversity were only affected by sampling season. Microbial metabolic activity and substrate utilization pattern, as well as soil moisture and temperature, did not show any apparent variations among stand ages. Pearson's correlation analysis indicated that both microbial metabolic activity of all 95 carbon sources (r=0.869; P<0.01) and the specific substrate metabolic activities (amides and amines: r=0.838, P<0.01; polymers: r=0.884, P<0.01; miscellaneous: r=0.895, P<0.01; carboxylic acids: r=0.910, P<0.01; amino acids: r=0.806, P<0.01; carbohydrates: r=0.808, P<0.01) were positively correlated with soil temperature. Metabolic diversity (r=0.806, P<0.01) and metabolic evenness (r=0.819, P<0.01) was positively correlated with soil temperature but metabolic richness (r=−0.517, P<0.05) was negatively correlated with soil moisture. Metabolic evenness was positively correlated with soil temperature (r=0.416, P<0.05). Seasonal changes in soil bacterial community were greater than those induced by girdling and stand age, and were tightly linked to seasonal soil microclimatic differences, such as soil moisture and temperature. The girdling treatment exerted a greater effect on soil bacterial communities during the dry season than in the rainy season. Our study illustrated that the response of bacterial substrate utilization profiles to changes in plant belowground carbon supply is seasonally dependent in subtropical Eucalyptus plantations.