Characterization of bacterial community structure in rhizosphere soil of grain legumes

Legacy effects override soil properties for CO2 and N2O but not CH4 emissions following digestate application to soil

The application of organic materials to soil can recycle nutrients and increase organic matter in agricultural lands. Digestate can be used as a nutrient source for crop production but it has also been shown to stimulate greenhouse gas (GHG) emissions from amended soils. While edaphic factors, such as soil texture and pH, have been shown to be strong determinants of soil GHG fluxes, the impact of the legacy of previous management practices is less well understood. Here we aim to investigate the impact of such legacy effects and to contrast them against soil properties to identify the key determinants of soil GHG fluxes following digestate application. Soil from an already established field experiment was used to set up a pot experiment, to evaluate N2O, CH4 and CO2 fluxes from cattle-slurry-digestate amended soils. The soil had been treated with farmyard manure, green manure or synthetic N-fertilizer, 18 months before the pot experiment was set up. Following homogenization and a preincubation stage, digestate was added at a concentration of 250 kg total N/ha eq. Soil GHG fluxes were then sampled over a 64 day period. The digestate stimulated emissions of the three GHGs compared to controls. The legacy of previous soil management was found to be a key determinant of CO2 and N2O flux while edaphic variables did not have a significant effect across the range of variables included in this experiment. Conversely, edaphic variables, in particular texture, were the main determinant of CH4 flux from soil following digestate application. Results demonstrate that edaphic factors and current soil management regime alone are not effective predictors of soil GHG flux response following digestate application. Knowledge of the site management in terms of organic amendments is required to make robust predictions of the likely soil GHG flux response following digestate application to soil.

Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management

Plants manipulate their rhizosphere community in a species and even a plant life stage-dependent manner. In essence plants select, promote and (de)activate directly the local bacterial and fungal community, and indirectly representatives of the next trophic level, protists and nematodes. By doing so, plants enlarge the pool of bioavailable nutrients and maximize local disease suppressiveness within the boundaries set by the nature of the local microbial community. MiSeq sequencing of specific variable regions of the 16S or 18S ribosomal DNA (rDNA) is widely used to map microbial shifts. As current RNA extraction procedures are time-consuming and expensive, the rRNA-based characterization of the active microbial community is taken along less frequently. Recently, we developed a relatively fast and affordable protocol for the simultaneous extraction of rDNA and rRNA from soil. Here, we investigated the long-term impact of three type of soil management, two conventional and an organic regime, on soil biota in fields naturally infested with the Columbian root-knot nematode Meloidogyne chitwoodi with pea (Pisum sativum) as the main crop. For all soil samples, large differences were observed between resident (rDNA) and active (rRNA) microbial communities. Among the four organismal group under investigation, the bacterial community was most affected by the main crop, and unweighted and weighted UniFrac analyses (explaining respectively 16.4% and 51.3% of the observed variation) pointed at a quantitative rather than a qualitative shift. LEfSe analyses were employed for each of the four organismal groups to taxonomically pinpoint the effects of soil management. Concentrating on the bacterial community in the pea rhizosphere, organic soil management resulted in a remarkable activation of members of the Burkholderiaceae, Enterobacteriaceae, and Pseudomonadaceae. Prolonged organic soil management was also accompanied by significantly higher densities of bacterivorous nematodes, whereas levels of M. chitwoodi had dropped drastically. Though present and active in the fields under investigation Orbiliaceae, a family harboring numerous nematophagous fungi, was not associated with the M. chitwoodi decline. A closer look revealed that a local accumulation and activation of Pseudomonas, a genus that includes a number of nematode-suppressive species, paralleled the lower M. chitwoodi densities. This study underlines the relevance of taking along both resident and active fractions of multiple organismal groups while mapping the impact of e.g. crops and soil management regimes.

Potential use of high-throughput sequencing of soil microbial communities for estimating the adverse effects of continuous cropping on ramie (Boehmeria nivea L. Gaud)

Ramie (Boehmeria nivea L. Gaud) fiber, one of the most important natural fibers, is extracted from stem bark. Continuous cropping is the main obstacle to ramie stem growth and a major cause of reduced yields. Root-associated microbes play crucial roles in plant growth and health. In this study, we investigated differences between microbial communities in the soil of healthy and continuously cropped ramie plants, and sought to identify potential mechanisms whereby these communities could counteract the problems posed by continuous cropping. Paired-end Illumina MiSeq analysis of 16S rRNA and ITS gene amplicons was employed to study bacterial and fungal communities. Long-term monoculture of ramie significantly decreased fiber yields and altered soil microbial communities. Our findings revealed how microbial communities and functional diversity varied according to the planting year and plant health status. Soil bacterial diversity increased with the period of ramie monoculture, whereas no significant differences were observed for fungi. Sequence analyses revealed that Firmicutes, Proteobacteria, and Acidobacteria were the most abundant bacterial phyla. Firmicutes abundance decreased with the period of ramie monoculture and correlated positively with the stem length, stem diameter, and fiber yield. The Actinobacteria, Chloroflexi, and Zygomycota phyla exhibited a significant (P < 0.05) negative correlation with yields during continuous cultivation. Some Actinobacteria members showed reduced microbial diversity, which prevented continuous ramie cropping. Ascomycota, Zygomycota, and Basidiomycota were the main fungal phyla. The relatively high abundance of Bacillus observed in healthy ramie may contribute to disease suppression, thereby promoting ramie growth. In summary, soil weakness and increased disease in ramie plants after long-term continuous cropping can be attributed to changes in soil microbes, a reduction in beneficial microbes, and an accumulation of harmful microbes.

Legume crop rotation suppressed nitrifying microbial community in a sugarcane cropping soil

Nitrifying microorganisms play an important role in nitrogen (N) cycling in agricultural soils as nitrification leads to accumulation of nitrate (NO3-) that is readily lost through leaching and denitrification, particularly in high rainfall regions. Legume crop rotation in sugarcane farming systems can suppress soil pathogens and improve soil health, but its effects on soil nitrifying microorganisms are not well understood. Using shotgun metagenomic sequencing, we investigated the impact of two legume break crops, peanut (Arachis hypogaea) and soybean (Glycine max), on the nitrifying communities in a sugarcane cropping soil. Cropping with either legume substantially increased abundances of soil bacteria and archaea and altered the microbial community composition, but did not significantly alter species richness and evenness relative to a bare fallow treatment. The ammonia oxidisers were mostly archaeal rather than bacterial, and were 24-44% less abundant in the legume cropping soils compared to the bare fallow. Furthermore, abundances of the archaeal amoA gene encoding ammonia monooxygenase in the soybean and peanut cropping soils were only 30-35% of that in the bare fallow. These results warrant further investigation into the mechanisms driving responses of ammonia oxidising communities and their nitrification capacity in soil during legume cropping.

Metagenomic evidence of stronger effect of stylo (legume) than bahiagrass (grass) on taxonomic and functional profiles of the soil microbial community

Plants are key determinants of soil microbial community (SMC). Legumes and grasses are distinct groups in various ecosystems; however, how they differentially shape SMC structure and functioning has yet to be explored. Here, we investigate SMC in soils grown with stylo (legume) or bahiagrass (grass). Soil metagenomic sequencing indicates that Archaea was more abundant in unplanted soils than in planted soils, and that stylo selected higher abundance of fungi than bahiagrass. When the stylo soils enriched Streptomyces, Frankia, Mycobacterium and Amycolatopsis, the bahiagrass soils enriched Sphingomonas and Sphingobium. NMDS reveals that the legume shaped SMC more greatly than the grass (P < 0.004). SMC functional profiles (KEGG and CAZy) were also greatly altered by plants with the legume being more effective (P < 0.000 and P < 0.000). The abundant microbial taxa contributed to the main community functions, with Conexibacter, Sphingomonas, and Burkholderia showing multifunctionality. Moreover, soil chemical property showed much higher direct effect on SMC structure and functional profiles than soil extracts, although the soil total nitrogen and some compounds (e.g. heptadecane, 1-pentadecyne and nonanoic acid) in soil extracts were best correlated with SMC structure and functional profiles. These findings are the first to suggest that legume species shape SMC more greatly than grass species.

Effects of plant-symbiotic relationships on the living soil microbial community and microbial necromass in a long-term agro-ecosystem

We examined the impact of arbuscular mycorrhizal fungi and rhizobia on the living microbial community and microbial necromass under different long-term fertilization treatments at the long-term Static Fertilization Experiment Bad Lauchstädt (Germany). Phospholipid fatty acids (PLFA) and amino sugars plus muramic acid, were used as biomarkers for soil microbial bio- and necromass, respectively, and analyzed from six treatments imposed on two crop rotations, varying only in the inclusion/non-inclusion of a legume. Treatments included: two levels of only farmyard manure (FYM), only mineral fertilizer (NPK), the combined application of both fertilizer types and a non-fertilized control. PLFA profiles differed clearly between the investigated crop rotations and were significantly related to labile C, mineral N, and soil pH. This emphasizes the role of carbon, and of mycorrhizal and rhizobial symbioses, as driver for changes in the microbial community composition due to effects on the living conditions in soil. We found some evidence that legume associated symbiosis with arbuscular mycorrhizal fungi and rhizobia act as a buffer, reducing the impact of varying inputs of mineral nutrients on the decomposer community. While our results support former findings that living microbial populations vary within short-term periods and are reflective of a given crop grown in a given year, soil necromass composition indicates longer term changes across the two crop rotation types, mainly shaped by fertilizer related effects on the community composition and C turnover. However, there was some evidence that specifically the presence of a legume, affects the soil necromass composition not only over the whole crop rotation but even in the short-term.

The interaction between iron nutrition, plant species and soil type shapes the rhizosphere microbiome

Plant-associated microorganisms can stimulate plants growth and influence both crops yield and quality by nutrient mobilization and transport. Therefore, rhizosphere microbiome appears to be one of the key determinants of plant health and productivity. The roots of plants have the ability to influence its surrounding microbiology, the rhizosphere microbiome, through the creation of specific chemical niches in the soil mediated by the release of phytochemicals (i.e. root exudates) that depends on several factors, such as plants genotype, soil properties, plant nutritional status, climatic conditions. In the present research, two different crop species, namely barley and tomato, characterized by different strategies for Fe acquisition, have been grown in the RHIZOtest system using either complete or Fe-free nutrient solution to induce Fe starvation. Afterward, plants were cultivated for 6 days on two different calcareous soils. Total DNA was extracted from rhizosphere and bulk soil and 454 pyrosequencing technology was applied to V1-V3 16S rRNA gene region. Approximately 5000 sequences were obtained for each sample. The analysis of the bacterial population confirmed that the two bulk soils showed a different microbial community. The presence of the two plant species, as well as the nutritional status (Fe-deficiency and Fe-sufficiency), could promote a differentiation of the rhizosphere microbiome, as highlighted by non-metric multidimensional scaling (NMDS) analysis. Alphaproteobacteria, Actinobacteria, Chloracidobacteria, Thermoleophilia, Betaproteobacteria, Saprospirae, Gemmatimonadetes, Gammaproteobacteria, Acidobacteria were the most represented classes in all the samples analyzed even though their relative abundance changed as a function of the soil, plant species and nutritional status. To our knowledge, this research demonstrate for the first time that different plants species with a diverse nutritional status can promote the development of a peculiar rhizosphere microbiome, depending on the growth substrate.

Bacterial Communities in the Rhizosphere of Amilaceous Maize (Zea mays L.) as Assessed by Pyrosequencing

Maize (Zea mays L.) is the staple diet of the native peasants in the Quechua region of the Peruvian Andes who continue growing it in small plots called chacras following ancestral traditions. The abundance and structure of bacterial communities associated with the roots of amilaceous maize has not been studied in Andean chacras. Accordingly, the main objective of this study was to describe the rhizospheric bacterial diversity of amilaceous maize grown either in the presence or the absence of bur clover cultivated in soils from the Quechua maize belt. Three 16S rRNA gene libraries, one corresponding to sequences of bacteria from bulk soil of a chacra maintained under fallow conditions, the second from the rhizosphere of maize-cultivated soils, and the third prepared from rhizospheric soil of maize cultivated in intercropping with bur clover were examined using pyrosequencing tags spanning the V4 and V5 hypervariable regions of the gene. A total of 26031 sequences were found that grouped into 5955 distinct operational taxonomic units which distributed in 309 genera. The numbers of OTUs in the libraries from the maize-cultivated soils were significantly higher than those found in the libraries from bulk soil. One hundred ninety seven genera were found in the bulk soil library and 234 and 203 were in those from the maize and maize/bur clover-cultivated soils. Sixteen out of the 309 genera had a relative abundance higher than 0.5% and the were (in decreasing order of abundance) Gp4, Gp6, Flavobacterium, Subdivision3 genera incertae sedis of the Verrucomicrobia phylum, Gemmatimonas, Dechloromonas, Ohtaekwangia, Rhodoferax, Gaiella, Opitutus, Gp7, Spartobacteria genera incertae sedis, Terrimonas, Gp5, Steroidobacter and Parcubacteria genera incertae sedis. Genera Gp4 and Gp6 of the Acidobacteria, Gemmatimonas and Rhodoferax were the most abundant in bulk soil, whereas Flavobacterium, Dechloromonas and Ohtaekwangia were the main genera in the rhizosphere of maize intercropped with bur clover, and Gp4, Subdivision3 genera incertae sedis of phylum Verrucomicrobia, Gp6 and Rhodoferax were the main genera in the rhizosphere of maize plants. Taken together, our results suggest that bur clover produces specific changes in rhizospheric bacterial diversity of amilaceous maize plants.

Stability and succession of the rhizosphere microbiota depends upon plant type and soil composition

We examined succession of the rhizosphere microbiota of three model plants (Arabidopsis, Medicago and Brachypodium) in compost and sand and three crops (Brassica, Pisum and Triticum) in compost alone. We used serial inoculation of 24 independent replicate microcosms over three plant generations for each plant/soil combination. Stochastic variation between replicates was surprisingly weak and by the third generation, replicate microcosms for each plant had communities that were very similar to each other but different to those of other plants or unplanted soil. Microbiota diversity remained high in compost, but declined drastically in sand, with bacterial opportunists and putative autotrophs becoming dominant. These dramatic differences indicate that many microbes cannot thrive on plant exudates alone and presumably also require carbon sources and/or nutrients from soil. Arabidopsis had the weakest influence on its microbiota and in compost replicate microcosms converged on three alternative community compositions rather than a single distinctive community. Organisms selected in rhizospheres can have positive or negative effects. Two abundant bacteria are shown to promote plant growth, but in Brassica the pathogen Olpidium brassicae came to dominate the fungal community. So plants exert strong selection on the rhizosphere microbiota but soil composition is critical to its stability. microbial succession/ plant-microbe interactions/rhizosphere microbiota/selection.

Isolation and characterization of bacteria from the rhizosphere and bulk soil of Stellera chamaejasme L

This study is the first to describe the composition and characteristics of culturable bacterial isolates from the rhizosphere and bulk soil of the medicinal plant Stellera chamaejasme L. at different growth stages. Using a cultivation-dependent approach, a total of 148 isolates showing different phenotypic properties were obtained from the rhizosphere and bulk soil. Firmicutes and Actinobacteria were the major bacterial groups in both the rhizosphere and bulk soil at all 4 growth stages of S. chamaejasme. The diversity of the bacterial community in the rhizosphere was higher than that in bulk soil in flowering and fruiting stages. The abundance of bacterial communities in the rhizosphere changed with the growth stages and had a major shift at the fruiting stage. Dynamic changes of bacterial abundance and many bacterial groups in the rhizosphere were similar to those in bulk soil. Furthermore, most bacterial isolates exhibited single or multiple biochemical activities associated with S. chamaejasme growth, which revealed that bacteria with multiple physiological functions were abundant and widespread in the rhizosphere and bulk soil. These results are essential (i) for understanding the ecological roles of bacteria in the rhizosphere and bulk soil and (ii) as a foundation for further evaluating their efficacy as effective S. chamaejasme growth-promoting rhizobacteria.

Interactions between Bacillus anthracis and plants may promote anthrax transmission

Environmental reservoirs are essential in the maintenance and transmission of anthrax but are poorly characterized. The anthrax agent, Bacillus anthracis was long considered an obligate pathogen that is dormant and passively transmitted in the environment. However, a growing number of laboratory studies indicate that, like some of its close relatives, B. anthracis has some activity outside of its vertebrate hosts. Here we show in the field that B. anthracis has significant interactions with a grass that could promote anthrax spore transmission to grazing hosts. Using a local, virulent strain of B. anthracis, we performed a field experiment in an enclosure within a grassland savanna. We found that B. anthracis increased the rate of establishment of a native grass (Enneapogon desvauxii) by 50% and that grass seeds exposed to blood reached heights that were 45% taller than controls. Further we detected significant effects of E. desvauxii, B. anthracis, and their interaction on soil bacterial taxa richness and community composition. We did not find any evidence for multiplication or increased longevity of B. anthracis in bulk soil associated with grass compared to controls. Instead interactions between B. anthracis and plants may result in increased host grazing and subsequently increased transmission to hosts.

Anthrax is a neglected zoonotic disease affecting livestock, wildlife, and humans in developing countries, particularly in Africa and Asia, and it occurs regularly in rural parts of North America. The causative agent of anthrax, Bacillus anthracis is transmitted by spores that persist for long periods of time in the environment. The transmission mechanisms of socioeconomically important and environmentally maintained pathogens are poorly understood, yet essential for understanding disease dynamics and devising appropriate control measures. Recent laboratory studies show that B. anthracis interacts with plants and other soil-dwelling organisms that may affect its survival and transmission. In this paper, we describe the results of a field experiment designed to test whether the interaction of B. anthracis with plants might affect its persistence and potential transmission to grazing hosts. We found that like some of its close relatives, B. anthracis promotes plant growth. Rather than simply lying in wait as a dormant spore in soil, instead B. anthracis may promote plant growth as a way of attracting hosts to graze on infectious material at carcass sites.

Isolation of rhizospheric and roots endophytic actinomycetes from Leguminosae plant and their activities to inhibit soybean pathogen, Xanthomonas campestris pv. glycine

In this study, actinomycetes from roots and rhizospheric soils of leguminous plants were isolated using starch casein agar supplemented with antifungal and antibacterial antibiotics. Three hundred and seventeen actinomycetes were isolated with 77 isolates obtained from plant roots and 240 isolates from rhizospheric soils. Analysis of whole-organism hydrolysates showed that 289 strains were rich in the LL-isomer of diaminopimelic acid, a result consistent with their assignment to the streptomycetes. The remaining 28 strains were assigned to non-streptomycetes based on the presence of meso-isomer of diaminopimelic acid in cell wall. Sixty-four isolates (20.2%) showed antagonistic activity against soybean pathogen Xanthomonas campestris pv. glycine by agar overlay method. Isolate RM 365 showed the highest activity with an inhibition ratio of 3.79, with no inhibitory activity on the growth of Rhizobium japonicum TISTR 079, Rhizobium sp. TISTR 061 and Rhizobium sp. TISTR 063. The 16S rRNA gene sequence analysis revealed that isolate RM 365 shared 99.28% similarity to Streptomyces caeruleatus GIMN4(T) (GQ329712). In addition, isolates which contained meso-DAP were also identified by 16S rRNA gene sequence analysis. The results showed that they were members of the genus Amycolatopsis, Isoptericola, Micromonospora, Microbispora, Nocardia, Nonomuraea, Promicromonospora and Pseudonocardia.

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

Plants host at the contact zone with soil a distinctive root-associated bacterial microbiota believed to function in plant nutrition and health. We investigated the diversity of the root microbiota within a phylogenetic framework of hosts: three Arabidopsis thaliana ecotypes along with its sister species Arabidopsis halleri and Arabidopsis lyrata, as well as Cardamine hirsuta, which diverged from the former ∼ 35 Mya. We surveyed their microbiota under controlled environmental conditions and of A. thaliana and C. hirsuta in two natural habitats. Deep 16S rRNA gene profiling of root and corresponding soil samples identified a total of 237 quantifiable bacterial ribotypes, of which an average of 73 community members were enriched in roots. The composition of this root microbiota depends more on interactions with the environment than with host species. Interhost species microbiota diversity is largely quantitative and is greater between the three Arabidopsis species than the three A. thaliana ecotypes. Host species-specific microbiota were identified at the levels of individual community members, taxonomic groups, and whole root communities. Most of these signatures were observed in the phylogenetically distant C. hirsuta. However, the branching order of host phylogeny is incongruent with interspecies root microbiota diversity, indicating that host phylogenetic distance alone cannot explain root microbiota diversification. Our work reveals within 35 My of host divergence a largely conserved and taxonomically narrow root microbiota, which comprises stable community members belonging to the Actinomycetales, Burkholderiales, and Flavobacteriales.

Host signature effect on plant root-associated microbiomes revealed through analyses of resident vs. active communities

Plant roots create specific microbial habitat in the soil - the rhizosphere. In this study, we characterized the rhizosphere microbiome of four host plant species to get insight into the impact of the host (host signature effect) on resident vs. active communities. Results show a distinct plant host specific signature found among wheat, maize, tomato and cucumber, based on the following three parameters: (i) each plant promoted the activity of a unique suite of soil bacterial populations; (ii) significant variations were observed in the number and the degree of dominance of active populations; and (iii) the level of contribution of active (rRNA-based) populations to the resident (DNA-based) community profiles. In the rhizoplane of all four plants, a significant reduction of diversity was observed, relative to the bulk soil. Moreover, an increase in DNA-RNA correspondence indicated higher representation of active bacterial populations in the residing rhizoplane community. This study demonstrates that the host plant determines the bacterial community composition in its immediate vicinity, especially with respect to the active populations.

Application of targeted metagenomics to explore abundance and diversity of CO₂-fixing bacterial community using cbbL gene from the rhizosphere of Arachis hypogaea

Sequestration of CO(2) by autotrophic bacteria is a key process of biogeochemical carbon cycling in soil ecosystem. Rhizosphere is a rich niche of microbial activity and diversity, influenced by change in atmospheric CO(2). Structural changes in rhizosphere composition influence microbial communities and the nutrient cycling. In the present study, the bacterial diversity and population dynamics were established using cbbL and 16S rRNA gene targeted metagenomics approach from the rhizosphere of Arachis hypogaea. A total of 108 cbbL clones were obtained from the rhizospheric soil which revealed predominance of cbbL sequences affiliated to Rhizobium leguminosarum, Bradyrhizobium sp., Sinorhizobium meliloti, Ochrobactrum anthropi and a variety of uncultured cbbL harboring bacteria. The 16S rRNA gene clone library exhibited the dominance of Firmicutes (34.4%), Proteobacteria (18.3%), Actinobacteria (17.2%) and Bacteroidetes (16.1%). About 43% nucleotide sequences of 16S rRNA gene clone library were novel genera which showed <95% homology with published sequences. Gene copy number of cbbL and 16S rRNA genes, determined by quantitative real-time PCR (qRT PCR), was 9.38 ± 0.75 × 10(7) and 5.43 ± 0.79 × 10(8) (per g dry soil), respectively. The results exhibited bacterial community structure with high bacterial diversity and abundance of CO(2)-fixing bacteria, which can be explored further for their role in carbon cycling, sustainable agriculture and environment management.

Hydrocarbon phytoremediation in the family Fabaceae--a review

Currently, studies often focus on the use of Poaceae species (grasses) for phytoremediation of hydrocarbon-contaminated soils. Research into the use of Fabaceae species (legumes) to remediate hydrocarbons in soils has been conducted, but these plants are commonly overlooked due to slower recorded rates of degradation compared with many grass species. Evidence in the literature suggests that in some cases Fabaceae species may increase total degradation of hydrocarbons and stimulate degradative capacity of the soil microbial community, particularly for contaminants which are normally more recalcitrant to degradation. As many recalcitrant hydrocarbons have negative impacts on human and ecosystem health, development of remediation options is crucial. Reconsideration of Fabaceae species for removal of such contaminants may lead to environmentally and economically sustainable technologies for remediation of contaminated sites.

Field trial assessment of biological, chemical, and physical responses of soil to tillage intensity, fertilization, and grazing

Soil microbial populations can fluctuate in response to environmental changes and, therefore, are often used as biological indicators of soil quality. Soil chemical and physical parameters can also be used as indicators because they can vary in response to different management strategies. A long-term field trial was conducted to study the effects of different tillage systems (NT: no tillage, DH: disc harrow, and MP: moldboard plough), P fertilization (diammonium phosphate), and cattle grazing (in terms of crop residue consumption) in maize (Zea mays L.), sunflower (Heliantus annuus L.), and soybean (Glycine max L.) on soil biological, chemical, and physical parameters. The field trial was conducted for four crop years (2000/2001, 2001/2002, 2002/2003, and 2003/2004). Soil populations of Actinomycetes, Trichoderma spp., and Gliocladium spp. were 49% higher under conservation tillage systems, in soil amended with diammonium phosphate (DAP) and not previously grazed. Management practices also influenced soil chemical parameters, especially organic matter content and total N, which were 10% and 55% higher under NT than under MP. Aggregate stability was 61% higher in NT than in MP, 15% higher in P-fertilized soil, and also 9% higher in not grazed strips, bulk density being 12% lower in NT systems compared with MP. DAP application and the absence of grazing also reduced bulk density (3%). Using conservation tillage systems, fertilizing crops with DAP, and avoiding grazing contribute to soil health preservation and enhanced crop production.

Plant age and genotype impact the progression of bacterial community succession in the Arabidopsis rhizosphere

The rhizosphere is strongly influenced by plant-derived phytochemicals exuded by roots and plant species exert a major selective force for bacteria colonizing the root-soil interface. We have previously shown that rhizobacterial recruitment is tightly regulated by plant genetics, by showing that natural variants of Arabidopsis thaliana support genotype-specific rhizobacterial communities while also releasing a unique blend of exudates at six weeks post-germination. To further understand how exudate release is controlled by plants, changes in rhizobacterial assemblages of two Arabidopsis accessions, Cvi and Ler where monitored throughout the plants' life cycle. Denaturing gradient gel electrophoresis (DGGE) fingerprints revealed that bacterial communities respond to plant derived factors immediately upon germination in an accession-specific manner. Rhizobacterial succession progresses differently in the two accessions in a reproducible manner. However, as plants age, rhizobacterial and control bulk soil communities converge, indicative of an attenuated rhizosphere effect, which coincides with the expected slow down in the active release of root exudates as plants reach the end of their life cycle. These data strongly suggest that exudation changes during plant development are highly genotype-specific, possibly reflecting the unique, local co-evolutionary communication processes that developed between Arabidopsis accessions and their indigenous microbiota.

Abundance and diversity of CO2-fixing bacteria in grassland soils close to natural carbon dioxide springs

Gaseous conditions at natural CO2 springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO2 concentrations ([CO2]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO2-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavesinci mofette, a natural CO2 spring which is known for very pure CO2 emissions, at different distances from the CO2 releasing vents, at locations that clearly differed in soil CO2 efflux (from 12.5 to over 200 micromol CO2 m(-2) s(-1) yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the "red-like" type of cbbL genes could be detected. In contrast, the "green-like" type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of "red-like" cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO2 concentrations. Furthermore, the diversity pattern of "red-like" cbbL genes changed depending on the CO(2) regime. This indicates that only a part of the autotrophic CO2-fixing microbes could adapt to the very high CO2 concentrations and adverse life conditions that are governed by mofette gaseous regime.

Influence of Arabidopsis thaliana accessions on rhizobacterial communities and natural variation in root exudates

Plant species is considered to be one of the most important factors in shaping rhizobacterial communities, but specific plant-microbe interactions in the rhizosphere are still not fully understood. Arabidopsis thaliana, for which a large number of naturally occurring ecotype accessions exist, lacks mycorrhizal associations and is hence an ideal model for rhizobacterial studies. Eight Arabidopsis accessions were found to exert a marked selective influence on bacteria associated with their roots, as determined by terminal-restriction fragment length polymorphism (T-RFLP) and ribosomal intergenic spacer analysis (RISA). Community differences in species composition and relative abundance were both significant (P <0.001). The eight distinct and reproducible accession-dependent community profiles also differed from control bulk soil. Root exudates of these variants were analysed by high performance liquid chromatography (HPLC) to try to establish whether the unique rhizobacterial assemblages among accessions could be attributed to plant-regulated chemical changes in the rhizosphere. Natural variation in root exudation patterns was clearly exhibited, suggesting that differences in exudation patterns among accessions could be influencing bacterial assemblages. Other factors such as root system architecture are also probably involved. Finally, to investigate the Arabidopsis rhizosphere further, the phylogenetic diversity of rhizobacteria from accession Cvi-0 is described.

Diversity of the Parachlamydiae in the Environment

Chlamydiae are obligate intracellular bacteria, parasites of a variety of eukaryotes ranging from amoebae to humans. Among them, the family Parachlamydiaceae comprises endosymbionts of amoebae, mainly Acanthamoeba, currently investigated as emerging pathogens of humans and other vertebrates. 16S rDNA-based PCR culture-independent studies in environmental samples have demonstrated the presence of Chlamydiales in various types of nonmedical habitats. Here we reviewed the biology of the Parachlamydiaceae, and more particularly those studies reporting molecular evidences for their presence in the environment, with a re-analysis of the 16S rDNA phylotypes.

How to get more out of molecular fingerprints: practical tools for microbial ecology

Community-level molecular techniques are widely used in comparative microbial ecology to assess the diversity of microbial communities and their response to changing environments. These include among others denaturing and temperature gradient gel electrophoresis (DGGE/TGGE), single-strand conformation polymorphism (SSCP), length heterogeneity-PCR (LH-PCR), terminal-restriction fragment length polymorphism (tRFLP) and 16S rRNA gene clone libraries. The amount of data derived from these techniques available in literature is continuously increasing and the lack of a universal way to interpret the raw fingerprint itself makes it difficult to compare between different results. Taking the DGGE technique as an example, we propose a setting-independent theoretical interpretation of the DGGE pattern, based on a straightforward processing on three levels of analysis: (i) the range-weighted richness (Rr) reflecting the carrying capacity of the system, (ii) the dynamics (Dy) reflecting the specific rate of species coming to significance, and (iii) functional organization (Fo), defined through a relation between the structure of a microbial community and its functionality. These Rr, Dy and Fo values, each representing a score to describe a microbial community, can be plotted in a 3D graph. The latter represents a visual ecological interpretation of the initial raw fingerprinting pattern.

Transcription dynamics of the functional tfdA gene during MCPA herbicide degradation by Cupriavidus necator AEO106 (pRO101) in agricultural soil

A modified protocol for simultaneous extraction of RNA and DNA, followed by real-time polymerase chain reaction quantification, was used to investigate tfdA gene expression during in situ degradation of the herbicide MCPA (4-chloro-2-methylphenoxy-acetic acid) in soil. tfdA encodes an alpha-ketoglutarate-dependent dioxygenase catalysing the first step in the degradation pathway of MCPA and 2,4-D (2,4-dichlorophenoxy-acetic acid). A linear recovery of tfdA mRNA over three orders of magnitude was shown, and the tfdA mRNA level was normalized using the tfdA mRNA/DNA ratio. The density of active cells required for tfdA mRNA detection was 10(5) cells g(-1) soil. Natural soil microcosms inoculated with Cupriavidus necator (formerly Ralstonia eutropha) AEO106 (pRO101) cells were amended with four different MCPA concentrations (2, 20, 50 and 150 mg kg(-1)). Mineralization rates were estimated by quantification of 14CO2 emission from degradation of 14C-MCPA. tfdA mRNA was detected 1 h after amendment at all four concentrations. In soils amended with 2 and 20 mg kg(-1), the mRNA/DNA ratio for tfdA demonstrated a sharp transient maximum of tfdA expression from no to full expression within 3 and 6 h respectively, followed by a decline and complete loss of expression after 19 and 43 h. A more complex pattern of tfdA expression was observed for the higher 50 and 150 mg kg(-1) amendments; this coincided with growth of C. necator AEO106 (pRO101) in the system. Repeated amendment with MCPA after 2 weeks in the 20 mg kg(-1) scenario revealed a sharp increase of tfdA mRNA, and absence of a mineralization lag phase. For all amendments, tfdA mRNA was detectable only during active mineralization, and thus revealed a direct correlation between tfdA mRNA presence and microbial degrader activity. The present study demonstrates that direct analysis of functional gene expression dynamics by quantification of mRNA can indeed be made in natural soil.

Frondicola australicus gen. nov., sp. nov., isolated from decaying leaf litter from a pine forest

An aerobic bacterium, designated strain E1HC-02T, was isolated from the decaying leaf litter of a slash pine forest located in southeast Queensland, Australia. Cells of strain E1HC-02T were short irregular rods (0.5–1.0×0.2–0.4 μm) which stained Gram-positive and possessed a cell-wall ultrastructure which appeared to be made of protein subunits. The novel strain grew optimally in 1 % trypticase soy broth (TSB) at 25 °C and at a pH of 9.1. Strain E1HC-02T metabolized a range of carbohydrates, organic acids and amino acids. The G+C content of the DNA was 71±1 mol% as determined by the thermal denaturation method. 16S rRNA gene sequence analysis of strain E1HC-02T showed that it was a member of the family Microbacteriaceae, phylum Actinobacteria. The cell wall contained a type B2β peptidoglycan, the dominant cellular fatty acid was 18 : 1ω7c and the major hydroxy fatty acid was 2-OH 14 : 0. The major menaquinones were MK-8 (76 %) and MK-7 (24 %) and the glycolipids present were disphosphatidylglycerol, phosphatidylglycerol and three unidentified phospholipids. The chemotaxonomic properties of strain E1HC-02T were distinctly different to all of the 17 genera of the family Microbacteriaceae and hence strain E1HC-02T is designated as representing a novel species of a new genus, Frondicola australicus gen. nov., sp. nov. The type strain of the type species is E1HC-02T (=JCM 13598T=DSM 17894T).

Quantitative isolation of biocontrol agents Trichoderma spp., Gliocladium spp. and actinomycetes from soil with culture media

Soil biodiversity plays a key role in the sustainability of agriculture systems and indicates the level of health of soil, especially when considering the richness of microorganisms that are involved in biological control of soilborne diseases. Cultural practices may produce changes in soil microflora, which can be quantified through the isolation of target microorganisms. Rhizosphere soil samples were taken from an assay with different crop rotations and tillage systems, and populations of Trichoderma spp., Gliocladium spp. and actinomycetes were quantified in order to select the general and selective culture media that better reflect the changes of these microbial populations in soil. The most efficient medium for the isolation of Trichoderma spp. and Gliocladium spp. was potato dextrose agar modified by the addition of chloramphenicol, streptomycin and rose bengal, and for actinomycetes was Küster medium, with cycloheximide and sodium propionate.

Diversity of transcripts of nitrite reductase genes (nirK and nirS) in rhizospheres of grain legumes

Transcription of the nirK and nirS genes coding for dissimilatory bacterial nitrite reductases was analyzed by reverse transcription PCR (RT-PCR) of mRNA isolated from rhizosphere samples of three economically important grain legumes at maturity: Vicia faba, Lupinus albus, and Pisum sativum. The nirK gene and transcripts could be detected in all the rhizosphere samples. In contrast, nirS could not be detected. Sampling variations were analyzed by comparing denaturing gradient gel electrophoresis profiles derived from nirK RT-PCR products. High similarity was observed between the replicates, and so one representative product per legume was cloned. Clones with the correct insert size were screened by restriction fragment length polymorphism by using the restriction enzyme MspI. The clones could be distributed into 12 different patterns. Patterns 1, 3, 4, 5, and 7 were common in clone libraries of the three rhizosphere types under study. Patterns 2, 9, 10, and 11 were absent from Pisum rhizospheres, while patterns 6, 8, and 12 were absent from the Vicia library. Pattern 1, which was the most dominant in the Vicia and Lupinus libraries, constituted about 25% of all clones. The Lupinus library had clones representing all 12 patterns, indicating it to be the most diverse among the three. Clones representative of each pattern were sequenced. All patterns grouped together forming a distinct cluster, which was divergent from previously described nirK sequences in the database. The study revealed a hitherto unknown diversity of denitrifiers in legume rhizospheres. A plant-dependent rhizosphere effect on the transcripts of a gene was evident.