Anaerobic nitrogen-fixing consortia consisting of clostridia isolated from gramineous plants

Underwater light source changes microecosystem constructed by Vallisneria spinulosa Yan for water restoration: Efficiency of water purification, characteristics of growth, and rhizosphere

Submerged macrophytes are effective in ecological restoration of water bodies polluted by nitrogen and phosphorus, and its restoration capacity depends on underwater illumination condition. This study explored the influencing mechanism of illumination on Vallisneria spinulosa Yan (V. spinulosa Yan) for water restoration. Addition of underwater light source increased the total nitrogen, ammonia nitrogen, total phosphorus, and phosphate removal loads of the V. spinulosa Yan growth system by 61.5, 39.2, 8.5, and 5.0 mg m-2 d-1, respectively. Meanwhile, the growth of V. spinulosa Yan was obviously promoted, even with high water turbidity. Although the biological nitrogen removal processes were inhibited by adding underwater light source, the growth of V. spinulosa Yan can be significantly improved, thus enhancing the efficiency of water purification via the absorption of nitrogen and phosphorus by V. spinulosa Yan. This study provides a theoretical foundation and technical support for application of submerged macrophytes in ecological water restoration.

Planting grass enhances relations between soil microbes and enzyme activities and restores soil functions in a degraded grassland

Introduction

Forage culture is a common way to restore degraded grasslands and soil functions, in which the reconstruction of the soil microbial community and its relationship with extracellular enzyme activity (EEAs) can characterize the recovery effects of degraded grasslands. However, the impacts of forage culture on the interaction between soil microbes and EEAs and whether the recovery effect of soil functions depends on the varying degradation statuses remain unclear.

Methods

We conducted a plantation of a dominant grass, Leymus chinensis, in the soil collected from severe, moderate, light, and non-degradation statuses in the Songnen grassland in northeastern China. We measured soil microbial diversity and soil EEAs, and predicted microbial functional groups using FUNGuild.

Results

The results showed that L. chinensis culture promoted soil bacterial alpha diversity and soil EEAs only in the moderate degradation status, indicating a dramatic dependence of the recovery effects of the grass culture on degradation status of the grassland. After planting L. chinensis for 10 weeks, a decreasing trend in the chemoheterotrophy and nitrate-reduction microbial functional groups was found. In contrast, the abundance of the nitrogen (N)-fixing microbial functional group tended to increase. The positive correlation between soil EEAs and the nitrate-reduction and N-fixing microbial functional groups was enhanced by planting L. chinensis, indicating that grass culture could promote soil N cycle functions.

Conclusion

We illuminate that grass culture may promote the restoration of soil functions, especially soil N cycling in degraded grasslands, and the recovery effect may depend on the grassland degradation status. We emphasized that selection of the plant species for restoration of grasslands needs to consider the restoration effects of microbial functional groups and soil functions.

Comparative genomic analysis and proposal of Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov., three novel Clostridium sensu stricto endophytes with diverse capabilities of acetic acid and ethanol production

OBJECTIVES

Genus Clostridium sensu stricto is generally regarded as the true Clostridium genus, which includes important human and animal pathogens and industrially relevant microorganisms. Besides, it is also a prominent member of plant-associated endophytes. However, our knowledge of endophytic Clostridium is limited.

METHODS

In this study, the endophytes were isolated under anaerobic condition from the roots of Paris polyphylla Smith var. yunnanensis. Subsequently, a polyphasic taxonomic approach was used to clarify their taxonomic positions. The fermentation products were measured in the isolates with HPLC analysis. Comparative genomics was performed on these new strains and other relatives.

RESULTS

In total, nine endophytic strains belonging to the genus Clostridium sensu stricto were isolated, and three of them were identified as new species. Seven of nine strains could produce acetate, propionate, and butyrate. Only two strains could produce ethanol, although genomics analysis suggested that only two of them were without genes for solventogenesis. Different from the endophytic strains, the phylogenetically closely related non-endophytic strains showed significant enrichment effects on some metabolic pathways involving environmental information processing, carbohydrate, and amino acid metabolisms, etc. It suggests that the genomes of these endophytic strains had undergone subtle changes associated with environmental adaptations.

CONCLUSION

Consequently, strains YIM B02505^T, YIM B02515^T, and YIM B02565^T are proposed to represent a new species of the genus Clostridium sensu stricto, for which the names Clostridium yunnanense sp. nov., Clostridium rhizosphaerae sp. nov., and Clostridium paridis sp. nov. are suggested.

Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth

Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of agroecological and circular economy approaches.

Silicone oil tamponade in managing recalcitrant endophthalmitis after cataract surgery secondary to Clostridium intestinale

A woman presented two weeks after uncomplicated cataract surgery with decreased visual acuity from endophthalmitis. One week after initial management with intravitreal antibiotics, her visual acuity decreased further, undergoing pars plana vitrectomy with intravitreal and intravenous antimicrobial coverage with preliminary improvement. Three days after vitrectomy, her vision decreased with recurrent inflammation. Initial cultures grew Clostridium intestinale She underwent repeat vitrectomy with silicone oil tamponade with no subsequent recurrence. The silicone oil was removed after 4 months and her visual acuity returned to 20/20 after 1 month and through 1 year of follow-up. Postoperative endophthalmitis is rare, with cases due to Clostridium species particularly destructive. In this first reported case of C. intestinale endophthalmitis, conventional management did not achieve lasting quiescence until silicone oil tamponade was employed. Pars plana vitrectomy with silicone oil tamponade should be considered in the management of recurrent endophthalmitis or endophthalmitis secondary to a recalcitrant microbe.

New insights into nitrogen removal potential in urban river by revealing the importance of microbial community succession on suspended particulate matter

The importance of suspended particulate matter (SPM) in nitrogen removal from aquatic environments has been acknowledged in recent years by recognizing the role of attached microbes. However, the succession of attached microbes on suspended particles and their role in nitrogen removal under specific surface microenvironment are still unknown. In this study, the causation among characteristics of SPM, composition and diversity of particle-attached microbial communities, and abundances of nitrogen-related genes in urban rivers was firstly quantitatively established by combing spectroscopy, 16 S rRNA amplicon sequencing, absolute gene quantification and supervised integrated machine learning. SPM in urban rivers, coated with organic layers, was mainly composed of silt and clay (87.59-96.87%) with D50 (medium particle size) of 8.636-30.130 μm. In terms of material composition of SPM, primary mineral was quartz and the four most abundant elements were O, Si, C, Al. The principal functional groups on SPM were hydroxyl and amide. Furthermore, samples with low, medium and high levels of ammoxidation potential were classified into three groups, among which significant differences of microbial communities were found. Samples were also separated into three groups with low, medium and high levels of denitrification potential and significant differences occurred among groups. The particle size, content of functional groups and concentration of SPM were identified as the most significant factors related with microbial communities, playing an important role in succession of particle-attached microbes. In addition, the path model revealed the significantly positive effect of organic matter and particle size on the microbial communities and potential nitrogen removal. The content of hydroxyl and temperature were identified as the most effective predicting factors for ammoxidation potential and denitrification potential respectively by Random Forests Regression models, which had good predictive performances for potential of ammoxidation (R² = 0.71) and denitrification (R² = 0.61). These results provide a basis for quickly assessing the ability of nitrogen removal in urban rivers.

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds

Seagrasses are marine angiosperms that can live completely or partially submerged in water and perform a variety of significant ecosystem services. Like terrestrial angiosperms, seagrasses can reproduce sexually and, the pollinated female flower develop into fruits and seeds, which represent a critical stage in the life of plants. Seed microbiomes include endophytic microorganisms that in terrestrial plants can affect seed germination and seedling health through phytohormone production, enhanced nutrient availability and defence against pathogens. However, the characteristics and origins of the seagrass seed microbiomes is unknown. Here, we examined the endophytic bacterial community of six microenvironments (flowers, fruits, and seeds, together with leaves, roots, and rhizospheric sediment) of the seagrass Halophila ovalis collected from the Swan Estuary, in southwestern Australia. An amplicon sequencing approach (16S rRNA) was used to characterize the diversity and composition of H. ovalis bacterial microbiomes and identify core microbiome bacteria that were conserved across microenvironments. Distinct communities of bacteria were observed within specific seagrass microenvironments, including the reproductive tissues (flowers, fruits, and seeds). In particular, bacteria previously associated with plant growth promoting characteristics were mainly found within reproductive tissues. Seagrass seed-borne bacteria that exhibit growth promoting traits, the ability to fix nitrogen and anti-pathogenic potential activity, may play a pivotal role in seed survival, as is common for terrestrial plants. We present the endophytic community of the seagrass seeds as foundation for the identification of potential beneficial bacteria and their selection in order to improve seagrass restoration.

Diversity and Variation of Asymbiotic Nitrogen-Fixing Microorganisms in Alpine Grasslands on the Tibetan Plateau

Asymbiotic nitrogen-fixing (ANF) bacteria contribute a substantial amount of nitrogen in ecosystems, especially in those with low symbiotic nitrogen fixation (SNF) capability. Degradation of alpine grassland is widespread on the Tibetan Plateau and sown grassland has become one of the main strategies for grassland restoration. However, the diversity and community structure of ANF bacteria in different grassland types remain unknown. The aim of this study was to fill this gap. Soil samples were obtained from 39 grassland plots selected from three counties in the eastern Tibetan Plateau. The plots were classified as natural grassland (NG), sown grassland (SG), lightly degraded grassland (LDG), and severely degraded grassland (SDG). ANF microbial communities of the four grassland types were compared at the level of community and species diversity by 16S rRNA high-throughput sequencing technology. The phylum Proteobacteria accounted for >72% of the ANF bacteria. The community structures of soil ANF bacteria differed significantly (p < 0.01) among grassland types. We concluded that: (1) planting gramineous forage could possibly mitigate the decrease in diversity of soil ANF bacteria caused by grassland degradation; and (2) the diversity of soil ANF bacteria in alpine grassland of the Tibetan Plateau is closely related to grassland degradation and restoration.

New insight to the role of microbes in the methane exchange in trees: evidence from metagenomic sequencing

Methane (CH₄ ) exchange in tree stems and canopies and the processes involved are among the least understood components of the global CH₄ cycle. Recent studies have focused on quantifying tree stems as sources of CH₄ and understanding abiotic CH₄ emissions in plant canopies, with the role of microbial in situ CH₄ formation receiving less attention. Moreover, despite initial reports revealing CH₄ consumption, studies have not adequately evaluated the potential of microbial CH₄ oxidation within trees. In this paper, we discuss the current level of understanding on these processes. Further, we demonstrate the potential of novel metagenomic tools in revealing the involvement of microbes in the CH₄ exchange of plants, and particularly in boreal trees. We detected CH₄ -producing methanogens and novel monooxygenases, potentially involved in CH₄ consumption, in coniferous plants. In addition, our field flux measurements from Norway spruce (Picea abies) canopies demonstrate both net CH₄ emissions and uptake, giving further evidence that both production and consumption are relevant to the net CH₄ exchange. Our findings, together with the emerging diversity of novel CH₄ -producing microbial groups, strongly suggest microbial analyses should be integrated in the studies aiming to reveal the processes and drivers behind plant CH₄ exchange.

Functional Interrelationships of Microorganisms in Iron-Based Anaerobic Wastewater Treatment

This study explicated the functional activities of microorganisms and their interrelationships under four previously reported iron reducing conditions to identify critical factors that governed the performance of these novel iron-dosed anaerobic biological wastewater treatment processes. Various iron-reducing bacteria (FeRB) and sulfate reducing bacteria (SRB) were identified as the predominant species that concurrently facilitated organics oxidation and the main contributors to removal of organics. The high organic contents of wastewater provided sufficient electron donors for active growth of both FeRB and SRB. In addition to the organic content, Fe (III) and sulfate concentrations (expressed by Fe/S ratio) were found to play a significant role in regulating the microbial abundance and functional activities. Various fermentative bacteria contributed to this FeRB-SRB synergy by fermenting larger organic compounds to smaller compounds, which were subsequently used by FeRB and SRB. Feammox (ferric reduction coupled to ammonium oxidation) bacterium was identified in the bioreactor fed with wastewater containing ammonium. Organic substrate level was a critical factor that regulated the competitive relationship between heterotrophic FeRB and Feammox bacteria. There were evidences that suggested a synergistic relationship between FeRB and nitrogen-fixing bacteria (NFB), where ferric iron and organics concentrations both promoted microbial activities of FeRB and NFB. A concept model was developed to illustrate the identified functional interrelationships and their governing factors for further development of the iron-based wastewater treatment systems.

Genotypic Variation of Endophytic Nitrogen-Fixing Activity and Bacterial Flora in Rice Stem Based on Sugar Content

Enhancement of the nitrogen-fixing ability of endophytic bacteria in rice is expected to result in improved nitrogen use under low-nitrogen conditions. Endophytic nitrogen-fixing bacteria require a large amount of energy to fix atmospheric nitrogen. However, it is unknown which carbon source and bacteria would affect nitrogen-fixing activity in rice. Therefore, this study examined genotypic variations in the nitrogen-fixing ability of rice plant stem as affected by non-structural carbohydrates and endophytic bacterial flora in field-grown rice. In the field experiments, six varieties and 10 genotypes of rice were grown in 2017 and 2018 to compare the acetylene reduction activity (nitrogen-fixing activity) and non-structural carbohydrates (glucose, sucrose, and starch) concentration in their stems at the heading stage. For the bacterial flora analysis, two genes were amplified using a primer set of 16S rRNA and nitrogenase (NifH) gene-specific primers. Next, acetylene reduction activity was correlated with sugar concentration among genotypes in both years, suggesting that the levels of soluble sugars influenced stem nitrogen-fixing activity. Bacterial flora analysis also suggested the presence of common and genotype-specific bacterial flora in both 16S rRNA and nifH genes. Similarly, bacteria classified as rhizobia, such as Bradyrhizobium sp. (Alphaproteobacteria) and Paraburkholderia sp. (Betaproteobacteria), were highly abundant in all rice genotypes, suggesting that these bacteria make major contributions to the nitrogen fixation process in rice stems. Gammaproteobacteria were more abundant in CG14 as well, which showed the highest acetylene reduction activity and sugar concentration among genotypes and is also proposed to contribute to the higher amount of nitrogen-fixing activity.

Abundance and community succession of nitrogen-fixing bacteria in ferrihydrite enriched cultures of paddy soils is closely related to Fe(III)-reduction

In flooded paddy soils, some metal reducers are also capable of nitrogen (N) fixation, which is essential in ensuring a reliable N-supply for rice growth. Microbial iron [Fe(III)] reduction is an important biogeochemical process that can be stimulated by ferrihydrite amendment to paddy soil. Therefore, this study aimed to investigate the abundance and succession of the N₂-fixing bacterial community in ferrihydrite enriched paddy soils collected from Hunan (HN) and Sichuan (SC) provinces, China. The relationship between the N₂-fixing bacterial community and Fe(III) reduction was also assessed. When compared with the control treatment, ferrihydrite enrichment significantly enhanced nitrogenase (nifH) gene abundance by 8.05 × 10⁵ to 4.45 × 10⁶ copies g^-1 soil during the 40-day flooding of HN soil, while nifH gene abundance in SC soil was remarkably increased by 5.90 × 10⁷ to 9.56 × 10⁷ copies g^-1 soil during day 1 to 5 in response to ferrihydrite amendment. The relative abundance of N₂-fixing bacteria peaked on day 5 (21.5% in HN soil and 5.4% in SC soil) and gradually decreased to a stable abundance after day 20. Remarkable increases in relative abundance of N₂-fixing bacteria during the first 10 days of flooding were detected in both soils with ferrihydrite enrichment, whereas little difference was found after day 10 of flooding. During the early stage of flooding, the Shannon and Simpson indexes of N₂-fixing bacteria with ferrihydrite enrichment were significantly decreased, and the community structure changed greatly. Most N₂-fixing bacteria in ferrihydrite enriched paddy soils were phylogenetically related to the order Clostridiales, with some of those potentially capable of Fe(III) reduction. The community succession of N₂-fixing bacteria closely correlated with Fe(III) reduction. Thus, improving N₂-fixation via stimulation of Fe(III) reduction might aid in the reduction of N-fertilizer application to paddy field.

Coupling between nitrogen-fixing and iron(III)-reducing bacteria as revealed by the metabolically active bacterial community in flooded paddy soils amended with glucose

Biological nitrogen fixation can contribute to maintaining the nitrogen balance and reducing the risk of environmental pollution caused by nitrogen fertilizer application in flooded paddy soils. Microorganisms associated with microbial iron [Fe(III)] reduction are prevalent and presumed to be closely linked with biological nitrogen fixation in flooded paddy soils. The relationship between the nitrogen-fixing bacteria (NFB) and Fe(III)-reducing bacteria (FeRB) and their responses to organic carbon addition were investigated based on the metabolically active bacterial community in flooded paddy soils amended with/without glucose (CK: 0 mol C kg^-1 soil; OC: 0.1 mol C kg^-1 soil). Both putative NFBs and FeRBs were affiliated to the phyla Firmicutes and Proteobacteria, which were the two most abundant phyla in the metabolically active bacterial community. Glucose addition remarkably altered the community structures of the putative NFBs and FeRBs during a 40-day incubation, and the relative abundances of putative NFBs and FeRBs in the OC treatment increased by 0.21%-1.62% and 2.22%-14.82% relative to the CK treatment, respectively, during the later stage of incubation. The putative FeRBs co-occurred with NFBs and hydrogen-oxidizing bacteria, and the relative abundances of NFBs and hydrogen-oxidizing bacteria showed significant positive correlation with that of respiratory FeRBs. Some FeRBs could also be capable of nitrogen fixation and/or hydrogen oxidation. Thus, it might be feasible to enhance biological nitrogen fixation efficiency by promoting the metabolic activities of FeRBs (such as by adding glucose), which contribute directly to biological nitrogen fixation associated with nitrogen-fixing Fe(III) reducers and indirectly by reducing the suppression of hydrogen on nitrogen fixation associated with hydrogen-dependent Fe(III) reducers.

Dairy soil bacterial responses to nitrogen application in simulated Italian ryegrass and white clover pasture

Through clearing and use of fertilizer and legumes, areas of southwestern Australia's unique coastal sand plains can support relatively low-cost dairies. However, the ancient, highly weathered nature of the soils in this region makes the dairies susceptible to a range of threats, including nutrient leaching and erosion. Despite this, Western Australian dairy cows typically produce up to 5,500 L of milk per head annually supported by inorganic nitrogen (N) fertilizer (commonly 50:50 urea and ammonium sulfate) at rates up to <320 kg of N/ha per year. Where hotspots exist (up to 2,000 kg of N/ha per year), total N exceeds pasture requirements. We investigated plant and soil bacteria responses to N fertilizer rates consistent with Australian legislated production practices on dairy farms for pure and mixed swards of white clover (Trifolium repens) and Italian ryegrass (Lolium multiflorum) in a long-term pasture experiment in controlled glasshouse conditions. Although the soil bacterial community structure at phylum level was similar for white clover and Italian ryegrass, relative abundances of specific subgroups of bacteria differed among plant species according to the N fertilizer regimen. Marked increases in relative abundance of some bacterial phyla and subphyla indicated potential inhibition of N cycling, especially for N hotspots in soil. Ammonium concentration in soil was less correlated with dominance of some N-cycling bacterial phyla than was nitrate concentration. Changes in bacterial community structure related to altered nutrient cycling highlight the potential for considering this area of research in policy assessment frameworks related to nutrient loads in dairy soils, especially for N.

Spatio-temporal dynamics of soil bacterial communities as a function of Amazon forest phenology

Most tropical evergreen rain forests are characterised by varying degrees of precipitation seasonality that influence plant phenology and litterfall dynamics. Soil microbes are sensitive to soil water:air ratio and to nutrient availability. We studied if within-year seasonality in precipitation and litterfall-derived nutrient input resulted in predictable seasonal variation in soil bacterial diversity/microbial functional groups in an Amazonian forest. We characterised the spatio-temporal dynamics of microbial communities from the plot to the stand scales and related them to precipitation seasonality and spatial variability in soil characteristics. Community composition and functional diversity showed high spatial heterogeneity and was related to variability in soil chemistry at the stand level. Large species turnover characterised plot level changes over time, reflecting precipitation seasonality-related changes in soil nutrient and moisture regimes. The abundance of decomposers was highest during the rainy season, characterised also by anaerobic saprophytes and N₂-fixers adapted to fluctuating redox conditions. In contrast, Beijerinckiaceae, likely derived from the phyllosphere, were found at higher abundances when litter inputs and accumulation were highest. We showed that in a mildly seasonal rain forest, the composition of soil microbial communities appears to be following canopy phenology patterns and the two are interlinked and drive soil nutrient availability.

Taxonomic structure and function of seed-inhabiting bacterial microbiota from common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.)

The present study investigated the endophytic bacterial communities in the seeds of mature, natural common reed (Phragmites australis) and narrowleaf cattail (Typha angustifolia L.). Additionally, seed endophytic bacterial communities were compared with rhizospheric and root endophytic bacterial communities using Illumina-based sequencing. Seed endophytic bacterial communities were dominated by Proteobacteria (reed, 41.24%; cattail, 45.51%), followed by Bacteroidetes (reed, 12.01%; cattail, 10.41%), Planctomycetes (reed, 10.36%; cattail, 9.09%), Chloroflexi (reed, 8.72%; cattail, 6.45%), Thermotogae (reed, 5.43%; cattail, 6.11%), Tenericutes (reed, 3.63%; cattail, 3.97%) and Spirochaetes (reed, 3.32%; cattail, 3.90%). The dominant genera were Desulfobacter (reed, 8.02%; cattail, 8.96%), Geobacter (reed, 2.74%; cattail, 2.81%), Thiobacillus (reed, 2.71%; cattail, 2.41%), Sulfurimonas (reed, 2.47%; cattail, 2.31%), Methyloversatilis (reed, 2.29%; cattail, 2.05%) and Dechloromonas (reed, 1.13%; cattail, 1.48%). Obvious distinctions were observed among the respective rhizospheric, root endophytic and seed endophytic bacterial communities. Principal coordinate analysis with weighted UniFrac distance and the heat map analysis demonstrated that the seed endophytic bacterial communities were distinct assemblages rather than a subgroup of rhizobacterial communities or root endophytic bacterial communities. These results provide new information regarding endophytic bacteria associated with seeds of wetland plants and demonstrate a variety of genera that have a strong potential to enhance phytoremediation in the wetland ecosystem.

Strong Regionality and Dominance of Anaerobic Bacterial Taxa Characterize Diazotrophic Bacterial Communities of the Arcto-Alpine Plant Species Oxyria digyna and Saxifraga oppositifolia

Arctic and alpine biomes are most often strongly nitrogen-limited, and hence biological nitrogen fixation is a strong driver of these ecosystems. Both biomes are characterized by low temperatures and short growing seasons, but they differ in seasonality of solar radiation and in soil water balance due to underlying permafrost in the Arctic. Arcto-alpine plant species are well-adapted to the low temperatures that prevail in their habitats, and plant growth is mainly limited by the availability of nutrients, in particular nitrogen, due to slow mineralization. Nitrogen fixing bacteria are likely important for plant growth in these habitats, but very little is known of these bacteria or forces shaping their communities. In this study, we characterized the potential nitrogen fixing bacterial (PNFB) communities associated with two arcto-alpine pioneer plant species, Oxyria digyna (mountain sorrel) and Saxifraga oppositifolia (blue saxifrage), in three climate regions. Both of these plants readily colonize low nutrient mineral soils. Our goal was to investigate how climate (region) and, on the other hand, host plant and plant species shape these communities. To our knowledge, this is the first comprehensive study describing PNFB communities associated with pioneer plants in different arcto-alpine biomes. Replicate samples were taken from two arctic regions, Kilpisjärvi and Ny-Ålesund, and one alpine region, Mayrhofen. In these, the PNFB communities in the bulk and rhizosphere soils and the plant endospheres were characterized by nifH-targeted PCR and massive parallel sequencing. The data revealed strong effects of climatic region on the dominating nitrogen fixers. Specifically, nifH sequences related to Geobacter (δ-Proteobacteria) were present in high relative abundances in the nitrogen-fixing communities in the Mayrhofen and Kilpisjärvi regions, while members of the Clostridiales prevailed in the Kilpisjärvi and Ny-Ålesund regions. The bulk and rhizosphere soil as well as the endosphere communities in the Mayrhofen region were all characterized by high relative abundances of nifH sequences related to Geobacter. In contrast, the endosphere and soil (bulk or rhizosphere soil) communities in the High Arctic were highly divergent: endosphere communities in the arctic regions were shaped by Clostridium spp., while nifH sequences representing δ-Proteobacteria, β-Proteobacteria, Cyanobacteria (in Ny-Ålesund), and Verrucomicrobia (in Kilpisjärvi) dominated the soil communities. Interestingly, the major PNFB genera identified in this study have been previously identified as members of conserved core microbiomes in the endospheres and seeds of these plants by 16S rRNA gene based analyses combined with bacterial isolation, suggesting a very tight interaction between diazotrophic bacteria and these arctic pioneer plants. Overall, anaerobic bacterial taxa dominated the PNFB communities of the endospheres and rhizospheres of the two plant species in all study sites. This could indicate anoxic conditions in and around plant roots at the time of sampling (early growth season), created by melting snow and underlying permafrost.

Plants Assemble Species Specific Bacterial Communities from Common Core Taxa in Three Arcto-Alpine Climate Zones

Evidence for the pivotal role of plant-associated bacteria to plant health and productivity has accumulated rapidly in the last years. However, key questions related to what drives plant bacteriomes remain unanswered, among which is the impact of climate zones on plant-associated microbiota. This is particularly true for wild plants in arcto-alpine biomes. Here, we hypothesized that the bacterial communities associated with pioneer plants in these regions have major roles in plant health support, and this is reflected in the formation of climate and host plant specific endophytic communities. We thus compared the bacteriomes associated with the native perennial plants Oxyria digyna and Saxifraga oppositifolia in three arcto-alpine regions (alpine, low Arctic and high Arctic) with those in the corresponding bulk soils. As expected, the bulk soil bacterial communities in the three regions were significantly different. The relative abundances of Proteobacteria decreased progressively from the alpine to the high-arctic soils, whereas those of Actinobacteria increased. The candidate division AD3 and Acidobacteria abounded in the low Arctic soils. Furthermore, plant species and geographic region were the major determinants of the structures of the endophere communities. The plants in the alpine region had higher relative abundances of Proteobacteria, while plants from the low- and high-arctic regions were dominated by Firmicutes. A highly-conserved shared set of ubiquitous bacterial taxa (core bacteriome) was found to occur in the two plant species. Burkholderiales, Actinomycetales and Rhizobiales were the main taxa in this core, and they were also the main contributors to the differences in the endosphere bacterial community structures across compartments as well as regions. We postulate that the composition of this core is driven by selection by the two plants.

Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health.

Systemic colonization of clover (Trifolium repens) by Clostridium botulinum strain 2301

In recent years, cases of botulism in cattle and other farm animals and also in farmers increased dramatically. It was proposed, that these cases could be affiliated with the spreading of compost or other organic manures contaminated with Clostridium botulinum spores on farm land. Thus, soils and fodder plants and finally farm animals could be contaminated. Therefore, the colonization behavior and interaction of the botulinum neurotoxin (BoNT D) producing C. botulinum strain 2301 and the non-toxin producing Clostridium sporogenes strain 1739 were investigated on clover (Trifolium repens) in a field experiment as well as in phytochamber experiments applying axenic and additionally soil based systems under controlled conditions. Plants were harvested and divided into root and shoot parts for further DNA isolation and polymerase chain reaction (PCR) assays; subsamples were fixed for fluorescence in situ hybridization analysis in combination with confocal laser scanning microscopy. In addition, we observed significant differences in the growth behavior of clover plants when inoculated with clostridial spores, indicating a plant growth promoting effect. Inoculated plants showed an increased growth index (shoot size, wet and dry weight) and an enlarged root system induced by the systemic colonization of clover by C. botulinum strain 2301. To target C. botulinum and C. sporogenes, 16S rDNA directed primers were used and to specifically detect C. botulinum, BoNT D toxin genes targeted primers, using a multiplex PCR approach, were applied. Our results demonstrate an effective colonization of roots and shoots of clover by C. botulinum strain 2301 and C. sporogenes strain 1739. Detailed analysis of colonization behavior showed that C. botulinum can occur as individual cells, in cell clusters and in microcolonies within the rhizosphere, lateral roots and within the roots tissue of clover.

Microbial population dynamics in response to Pectobacterium atrosepticum infection in potato tubers

Endophytes are microbes and fungi that live inside plant tissues without damaging the host. Herein we examine the dynamic changes in the endophytic bacterial community in potato (Solanum tuberosum) tuber in response to pathogenic infection by Pectobacterium atrosepticum, which causes soft rot in numerous economically important crops. We quantified community changes using both cultivation and next-generation sequencing of the 16S rRNA gene and found that, despite observing significant variability in both the mass of macerated tissue and structure of the endophytic community between individual potato tubers, P. atrosepticum is always taken over by the endophytes during maceration. 16S rDNA sequencing revealed bacteria from the phyla Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, Verrucomicrobia, Acidobacteria, TM7, and Deinococcus-Thermus. Prior to infection, Propionibacterium acnes is frequently among the dominant taxa, yet is out competed by relatively few dominant taxa as the infection proceeds. Two days post-infection, the most abundant sequences in macerated potato tissue are Gammaproteobacteria. The most dominant genera are Enterobacter and Pseudomonas. Eight days post-infection, the number of anaerobic pectolytic Clostridia increases, probably due to oxygen depletion. These results demonstrate that the pathogenesis is strictly initiated by the pathogen (sensu stricto) and proceeds with a major contribution from the endophytic community.

Hygienisation and nutrient conservation of sewage sludge or cattle manure by lactic acid fermentation

Manure from animal farms and sewage sludge contain pathogens and opportunistic organisms in various concentrations depending on the health of the herds and human sources. Other than for the presence of pathogens, these waste substances are excellent nutrient sources and constitute a preferred organic fertilizer. However, because of the pathogens, the risks of infection of animals or humans increase with the indiscriminate use of manure, especially liquid manure or sludge, for agriculture. This potential problem can increase with the global connectedness of animal herds fed imported feed grown on fields fertilized with local manures. This paper describes a simple, easy-to-use, low-tech hygienization method which conserves nutrients and does not require large investments in infrastructure. The proposed method uses the microbiotic shift during mesophilic fermentation of cow manure or sewage sludge during which gram-negative bacteria, enterococci and yeasts were inactivated below the detection limit of 3 log10 cfu/g while lactobacilli increased up to a thousand fold. Pathogens like Salmonella, Listeria monocytogenes, Staphylococcus aureus, E. coli EHEC O:157 and vegetative Clostridium perfringens were inactivated within 3 days of fermentation. In addition, ECBO-viruses and eggs of Ascaris suum were inactivated within 7 and 56 days, respectively. Compared to the mass lost through composting (15-57%), the loss of mass during fermentation (< 2.45%) is very low and provides strong economic and ecological benefits for this process. This method might be an acceptable hygienization method for developed as well as undeveloped countries, and could play a key role in public and animal health while safely closing the nutrient cycle by reducing the necessity of using energy-inefficient inorganic fertilizer for crop production.

Characterization of leaf blade- and leaf sheath-associated bacterial communities and assessment of their responses to environmental changes in CO₂, temperature, and nitrogen levels under field conditions

Rice shoot-associated bacterial communities at the panicle initiation stage were characterized and their responses to elevated surface water-soil temperature (ET), low nitrogen (LN), and free-air CO2 enrichment (FACE) were assessed by clone library analyses of the 16S rRNA gene. Principal coordinate analyses combining all sequence data for leaf blade- and leaf sheath-associated bacteria revealed that each bacterial community had a distinct structure, as supported by PC1 (61.5%), that was mainly attributed to the high abundance of Planctomycetes in leaf sheaths. Our results also indicated that the community structures of leaf blade-associated bacteria were more sensitive than those of leaf sheath-associated bacteria to the environmental factors examined. Among these environmental factors, LN strongly affected the community structures of leaf blade-associated bacteria by increasing the relative abundance of Bacilli. The most significant effect of FACE was also observed on leaf blade-associated bacteria under the LN condition, which was explained by decreases and increases in Agrobacterium and Pantoea, respectively. The community structures of leaf blade-associated bacteria under the combination of FACE and ET were more similar to those of the control than to those under ET or FACE. Thus, the combined effects of environmental factors need to be considered in order to realistically assess the effects of environmental changes on microbial community structures.

Bacterial-biota dynamics of eight bryophyte species from different ecosystems

Despite the importance of bryophyte-associated microorganisms in various ecological aspects including their crucial roles in the soil-enrichment of organic mass and N2 fixation, nonetheless, little is known about the microbial diversity of the bryophyte phyllospheres (epi-/endophytes). To get insights into bacterial community structures and their dynamics on the bryophyte habitats in different ecosystems and their potential biological roles, we utilized the 16S rRNA gene PCR-DGGE and subsequent phylogenetic analyses to investigate the bacterial community of eight bryophyte species collected from three distinct ecosystems from western Japan. Forty-two bacterial species belonging to γ-proteobacteria and Firmicutes with 71.4% and 28.6%, respectively, were identified among 90 DGGE gel band population. These DGGE-bands were assigned to 13 different genera with obvious predomination the genus Clostridium with 21.4% from the total bacterial community. These analyses provide new insights into bryophyte-associated bacteria and their relations to the ecosystems.

Investigation of the bacterial retting community of kenaf (Hibiscus cannabinus) under different conditions using next-generation semiconductor sequencing

The microbial communities associated with kenaf (Hibiscus cannabinus) plant fibers during retting were determined in an effort to identify possible means of accelerating this process for industrial scale-up. Microbial communities were identified by semiconductor sequencing of 16S rRNA gene amplicons from DNA harvested from plant-surface associated samples and analyzed using an Ion Torrent PGM. The communities were sampled after 96 h from each of three different conditions, including amendments with pond water, sterilized pond water, or with a mixture of pectinolytic bacterial isolates. Additionally, plants from two different sources and having different pretreatment conditions were compared. We report that the best retting communities are dominated by members of the order Clostridiales. These bacteria appear to be naturally associated with the plant material, although slight variations between source materials were found. Additionally, heavy inoculations of pectinolytic bacteria established themselves and in addition their presence facilitated the rapid dominance of the original plant-associated Clostridiales. These data suggest that members of the order Clostridiales dominate the community and are most closely associated with efficient and effective retting. The results further suggest that establishment of the community structure is first driven by the switch to anaerobic conditions, and subsequently by possible competition for nitrogen. These findings reveal important bacterial groups involved in fiber retting, and suggest mechanisms for the manipulation of the community and retting efficiency by modifying nutrient availability.

Endophytic bacteria in the rice plant

Endophytic bacteria are defined as bacteria detected inside surface-sterilized plants or extracted from inside plants and having no visibly harmful effects on the plants. Various kinds of endophytic bacteria, such as Pantoea, Methylobacterium, Azospirillum, Herbaspirillum, Burkholderia and Rhizobium etc., have been found inside rice plants. This minireview summarizes and discusses recent studies of endophytic bacteria residing in rice plants, focusing on flora, origin, movement, and interaction with plants/other microbes and referring to endophytes in other plants. The findings concerning bacterial flora obtained by cultural and non-cultural methods are also compared and discussed. Some attempts to apply endophytes to the rice plant and the resultant effects are introduced. The future perspective to deepen the study of endophytes in terms of both application and basic science is considered.

Pyrosequencing reveals bacteria carried in different wind-eroded sediments

Little is known about the microbial communities carried in wind-eroded sediments from various soil types and land management systems. The novel technique of pyrosequencing promises to expand our understanding of the microbial diversity of soils and eroded sediments because it can sequence 10 to 100 times more DNA fragments than previous techniques, providing enhanced exploration into what microbes are being lost from soil due to wind erosion. Our study evaluated the bacterial diversity of two types of wind-eroded sediments collected from three different organic-rich soils in Michigan using a portable field wind tunnel. The wind-eroded sediments evaluated were a coarse sized fraction with 66% of particles >106 μm (coarse eroded sediment) and a finer eroded sediment with 72% of particles <106 μm. Our findings suggested that (i) bacteria carried in the coarser sediment and fine dust were effective fingerprints of the source soil, although their distribution may vary depending on the soil characteristics because certain bacteria may be more protected in soil surfaces than others; (ii) coarser wind-eroded sediment showed higher bacterial diversity than fine dust in two of the three soils evaluated; and (iii) certain bacteria were more predominant in fine dust (, , and ) than coarse sediment ( and ), revealing different locations and niches of bacteria in soil, which, depending on wind erosion processes, can have important implications on the soil sustainability and functioning. Infrared spectroscopy showed that wind erosion preferentially removes particular kinds of C from the soil that are lost via fine dust. Our study shows that eroded sediments remove the active labile organic soil particulates containing key microorganisms involved in soil biogeochemical processes, which can have a negative impact on the quality and functioning of the source soil.

Analysis of diversity of diazotrophic bacteria associated with the rhizosphere of a tropical Arbor, Melastoma malabathricum L

The diversity of diazotrophic bacteria in the rhizosphere of Melastoma malabathricum L. was investigated by cloning-sequencing of the nifH gene directly amplified from DNA extracted from soil. Samples were obtained from the rhizosphere and bulk soil of M. malabathricum growing in three different soil types (acid sulfate, peat and sandy clay soils) located very close to each other in south Kalimantan, Indonesia. Six clone libraries were constructed, generated from bulk and rhizosphere soil samples, and 300 nifH clones were produced, then assembled into 29 operational taxonomic units (OTUs) based on percent identity values. Our results suggested that nifH gene diversity is mainly dependent on soil properties, and did not differ remarkably between the rhizosphere and bulk soil of M. malabathricum except in acid sulfate soil. In acid sulfate soil, as the Shannon diversity index was lower in rhizosphere than in bulk soil, it is suggested that particular bacterial species might accumulate in the rhizosphere.

Nitrogen fixation associated with sago (Metroxylon sagu) and some implications

AIMS

To determine the presence and contribution of diazotrophic bacteria to nitrogen concentrations in edible starch derived from the sago palm (Metroxylon sagu).

METHODS AND RESULTS

Isolation of diazotrophic bacteria and analysis of nitrogen fixation were conducted on pith, root and sago starch samples. Acetylene reduction showed that five of ten starch samples were fixing nitrogen. Two presumptive nitrogen-fixing bacteria from starch fixed nitrogen in pure culture and five isolates were positive for the nif H gene. Nitrogen concentrations in 51 starch samples were low (37 samples <0·2 g kg(-1); 14 ranging from 0·2 to 2·0 g kg(-1)).

CONCLUSIONS

Nitrogen fixation occurs in sago starch, which undoubtedly plays a role in fermentation ecology. Nitrogen levels are considered too low to be of nutritional benefit and to protect against nutritional-associated illnesses.

SIGNIFICANCE AND IMPACT OF THE STUDY

Sago starch does not add significantly to the protein calorie intake and may be associated with susceptibility to nutritional-associated illness.

Endophytic bacterial diversity in roots of Phragmites australis in constructed Beijing Cuihu Wetland (China)

The community structure and diversity of endophytic bacteria in reed (Phragmites australis) roots growing in the Beijing Cuihu Wetland, China was investigated using the 16S rRNA library technique. Primers 799f and 1492r were used to amplify the specific bacterial 16S rRNA fragments successfully and construct the clone library. In total, 166 individual sequences were verified by colony PCR and used to assess the diversity of endophytic bacteria in reed roots. Phylogenetic analysis revealed that 78.9% of the clones were affiliated with Proteobacteria and included all five classes. Other clones belonged to Firmicutes (9.0%), Cytophaga/Flexibacter/Bacteroids (6.6%), Fusobacteria (2.4%), and nearly 3.0% were unidentified bacteria. In Proteobacteria, the Alpha and Gamma subgroups were the most abundant, accounting for approximately 34.4% and 31.3% of all Proteobacteria, respectively, and the dominant genera included Pleomorphomonas, Azospirillum, and Aeromonas. In addition, nearly 13.6% of the Proteobacteria were very similar to some genera of sulfate-reducing bacteria (SRB) such as Dechloromonas, Desulfovibrio, and Sulfurospirillum. The bacteria in these genera are considered to play important roles in the metabolism of nitrogen, phosphorus, sulfur, and some organic compounds in wetland systems. Hence, this study demonstrates that within the diverse bacterial communities found in reed roots, endophytic strains might have a strong potential to enhance phytoremediation by reed wetlands.

Bacterial gene abundances as indicators of greenhouse gas emission in soils

Nitrogen fixing and denitrifying bacteria, respectively, control bulk inputs and outputs of nitrogen in soils, thereby mediating nitrogen-based greenhouse gas emissions in an ecosystem. Molecular techniques were used to evaluate the relative abundances of nitrogen fixing, denitrifying and two numerically dominant ribotypes (based on the > or =97% sequence similarity at the 16S rRNA gene) of bacteria in plots representing 10 agricultural and other land-use practices at the Kellogg biological station long-term ecological research site. Quantification of nitrogen-related functional genes (nitrite reductase, nirS; nitrous oxide reductase, nosZ; and nitrogenase, nifH) as well as two dominant 16S ribotypes (belonging to the phyla Acidobacteria, Thermomicrobia) allowed us to evaluate the hypothesis that microbial community differences are linked to greenhouse gas emissions under different land management practices. Our results suggest that the successional stages of the ecosystem are strongly linked to bacterial functional group abundance, and that the legacy of agricultural practices can be sustained over decades. We also link greenhouse gas emissions with specific compositional responses in the soil bacterial community and assess the use of denitrifying gene abundances as proxies for determining nitrous oxide emissions from soils.

The Gram-positive side of plant-microbe interactions

Plant growth and development are significantly influenced by the presence and activity of microorganisms. To date, the best-studied plant-interacting microbes are Gram-negative bacteria, but many representatives of both the high and low G+C Gram-positives have excellent biocontrol, plant growth-promoting and bioremediation activities. Moreover, actinorhizal symbioses largely contribute to the global biological nitrogen fixation and many Gram-positive bacteria promote other types of symbioses in tripartite interactions. Finally, several prominent and devastating phytopathogens are Gram-positive. We summarize the present knowledge of the beneficial and detrimental interactions of Gram-positive bacteria with plants to underline the importance of this particular group of bacteria.

High rate of N2 fixation by East Siberian cryophilic soil bacteria as determined by measuring acetylene reduction in nitrogen-poor medium solidified with gellan gum

For evaluating N(2) fixation of diazotrophic bacteria, nitrogen-poor liquid media supplemented with at least 0.5% sugar and 0.2% agar are widely used for acetylene reduction assays. In such a soft gel medium, however, many N(2)-fixing soil bacteria generally show only trace acetylene reduction activity. Here, we report that use of a N(2) fixation medium solidified with gellan gum instead of agar promoted growth of some gellan-preferring soil bacteria. In a soft gel medium solidified with 0.3% gellan gum under appropriate culture conditions, bacterial microbiota from boreal forest bed soils and some free-living N(2)-fixing soil bacteria isolated from the microbiota exhibited 10- to 200-fold-higher acetylene reduction than those cultured in 0.2% agar medium. To determine the N(2) fixation-activating mechanism of gellan gum medium, qualitative differences in the colony-forming bacterial components from tested soil microbiota were investigated in plate cultures solidified with either agar or gellan gum for use with modified Winogradsky's medium. On 1.5% agar plates, apparently cryophilic bacterial microbiota showed strictly distinguishable microbiota according to the depth of soil in samples from an eastern Siberian Taiga forest bed. Some pure cultures of proteobacteria, such as Pseudomonas fluorescens and Burkholderia xenovorans, showed remarkable acetylene reduction. On plates solidified with 1.0% gellan gum, some soil bacteria, including Luteibacter sp., Janthinobacterium sp., Paenibacillus sp., and Arthrobacter sp., uniquely grew that had not grown in the presence of the same inoculants on agar plates. In contrast, Pseudomonas spp. and Burkholderia spp. were apparent only as minor colonies on the gellan gum plates. Moreover, only gellan gum plates allowed some bacteria, particularly those isolated from the shallow organic soil layer, to actively swarm. In consequence, gellan gum is a useful gel matrix to bring out growth potential capabilities of many soil diazotrophs and their consortia in communities of soil bacteria.

Molecular diversity analysis and bacterial population dynamics of an adapted seawater microbiota during the degradation of Tunisian zarzatine oil

The indigenous microbiota of polluted coastal seawater in Tunisia was enriched by increasing the concentration of zarzatine crude oil. The resulting adapted microbiota was incubated with zarzatine crude oil as the only carbon and energy source. Crude oil biodegradation capacity and bacterial population dynamics of the microbiota were evaluated every week for 28 days (day 7, day 14, day 21, and day 28). Results show that the percentage of petroleum degradation was 23.9, 32.1, 65.3, and 77.8%, respectively. At day 28, non-aromatic and aromatic hydrocarbon degradation rates reached 92.6 and 68.7%, respectively. Bacterial composition of the adapted microflora was analysed by 16S rRNA gene cloning and sequencing, using total genomic DNA extracted from the adapted microflora at days 0, 7, 14, 21, and 28. Five clone libraries were constructed and a total of 430 sequences were generated and grouped into OTUs using the ARB software package. Phylogenetic analysis of the adapted microbiota shows the presence of four phylogenetic groups: Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes. Diversity indices show a clear decrease in bacterial diversity of the adapted microflora according to the incubation time. The Proteobacteria are the most predominant (>80%) at day 7, day 14 and day 21 but not at day 28 for which the microbiota was reduced to only one OTU affiliated with the genus Kocuria of the Actinobacteria. This study shows that the degradation of zarzatine crude oil components depends on the activity of a specialized and dynamic seawater consortium composed of different phylogenetic taxa depending on the substrate complexity.

Sources of clostridia in raw milk on farms

A PCR-denaturing gradient gel electrophoresis (DGGE) method was used to examine on-farm sources of Clostridium cluster I strains in four dairy farms over 2 years. Conventional microbiological analysis was used in parallel to monitor size of clostridial populations present in various components of the milk production chain (soil, forage, grass silage, maize silage, dry hay, and raw milk). PCR amplification with Clostridium cluster I-specific 16S rRNA gene primers followed by DGGE separation yielded a total of 47 operational taxonomic units (OTUs), which varied greatly with respect to frequency of occurrence. Some OTUs were found only in forage, and forage profiles differed according to farm location (southern or northern Québec). More clostridial contamination was found in maize silage than in grass silage. Milk represented a potential environment for certain OTUs. No OTU was milk specific, indicating that OTUs originated from other environments. Most (83%) of the OTUs detected in raw milk were also found in grass or maize silage. Milk DGGE profiles differed according to farm and sampling year and fit into two distinct categories. One milk profile category was characterized by the presence of a few dominant OTUs, the presence of which appeared to be more related to farm management than to feed contamination. OTUs were more varied in the second profile category. The identities of certain OTUs frequently found in milk were resolved by cloning and sequencing. Clostridium disporicum was identified as an important member of clostridial populations transmitted to milk. Clostridium tyrobutyricum was consistently found in milk and was widespread in the other farm environments examined.

Endophytic bacterial diversity in rice (Oryza sativa L.) roots estimated by 16S rDNA sequence analysis

The endophytic bacterial diversity in the roots of rice (Oryza sativa L.) growing in the agricultural experimental station in Hebei Province, China was analyzed by 16S rDNA cloning, amplified ribosomal DNA restriction analysis (ARDRA), and sequence homology comparison. To effectively exclude the interference of chloroplast DNA and mitochondrial DNA of rice, a pair of bacterial PCR primers (799f-1492r) was selected to specifically amplify bacterial 16S rDNA sequences directly from rice root tissues. Among 192 positive clones in the 16S rDNA library of endophytes, 52 OTUs (Operational Taxonomic Units) were identified based on the similarity of the ARDRA banding profiles. Sequence analysis revealed diverse phyla of bacteria in the 16S rDNA library, which consisted of alpha, beta, gamma, delta, and epsilon subclasses of the Proteobacteria, Cytophaga/Flexibacter/Bacteroides (CFB) phylum, low G+C gram-positive bacteria, Deinococcus-Thermus, Acidobacteria, and archaea. The dominant group was Betaproteobacteria (27.08% of the total clones), and the most dominant genus was Stenotrophomonas. More than 14.58% of the total clones showed high similarity to uncultured bacteria, suggesting that nonculturable bacteria were detected in rice endophytic bacterial community. To our knowledge, this is the first report that archaea has been identified as endophytes associated with rice by the culture-independent approach. The results suggest that the diversity of endophytic bacteria is abundant in rice roots.

Diverse endophytic nitrogen-fixing bacteria isolated from wild rice Oryza rufipogon and description of Phytobacter diazotrophicus gen. nov. sp. nov

Twenty-three nitrogen-fixing bacteria were isolated from surface-sterilized stems and roots of wild rice Oryza rufipogon. Four clusters were defined among these bacteria by SDS-PAGE protein patterns and further confirmed by IS-PCR finger-printing analysis. Phylogenetic analysis of 16S rRNA gene sequences showed that the representative strains LS 8 and LS 18 of cluster II formed a monophyletic group sharing 94.0-97.3% similarities with defined enterobacterial species within the genera Salmonella, Citrobacter, Pantoea, Klebsiella, and Enterobacter. DNA-DNA hybridization, physiological, biochemical tests, and cell morphology also revealed that these strains could be differentiated from the related enterobacterial species. Based upon these results, we propose Phytobacter diazotrophicus gen. nov., sp. nov. to the bacterial group represented by strains LS 8 and LS 18. The type strain is LS 8(T) (=DSM 17806(T) = LMG 23328(T) = CGMCC 1.5339(T)). The DNA G+C content of strain LS 8(T) is 58.6 +/- 0.5 mol%.

Persistence and mobility of a Clostridium botulinum spore population introduced to soil with spiked compost

In a recent study it could be shown that compost samples can contain Clostridium botulinum. It was investigated if C. botulinum introduced with compost into botulinum-free soil can persist and be translocated within the soil. Compost was spiked with two C. botulinum type D spore concentrations (10(3) and 10(5) spores g(-1)) and the composts were spread on an experimental site. Over a period of 939 days, samples were taken from the upper (0-5 cm) and the lower (10-30 cm) soil horizons. Physical and chemical as well as microbiological variables were measured. Clostridium botulinum spores were quantified in a culture MPN-PCR assay. On day 757 the last positive sample was obtained in the plots with the lower spore concentration (10(3) g(-1)). The bacteria were never detected in the samples taken from the lower horizons of these plots. Clostridium botulinum persisted over the whole investigation period in the plots which were treated with compost spiked with 10(5) spores g(-1). The concentrations found were between 20 and 20,000 spores g(-1) soil. The bacteria were vertically translocated and could be found in the lower soil horizons (20-2000 spores g(-1) soil) starting 70 days after the compost was spread.

Expression of the nifH gene of a Herbaspirillum endophyte in wild rice species: daily rhythm during the light-dark cycle

The expression of nitrogenase genes of Herbaspirillum sp. B501 associated in shoot (leaf and stem) of wild rice, Oryza officinalis, was studied by means of reverse transcription-PCR (RT-PCR) targeted at the nifH gene. RT-PCR analyses indicate that nifH transcript was detected exclusively from nitrogen-fixing cells of gfp-tagged strain B501gfp1 in both free-living and endophytic states by using a constitutive gfp gene transcript as a positive control. Transcription of nifH and nitrogen fixation in free-living cells were induced maximally at a 2% O2 concentration and repressed in free air (21% O2). nifH transcription was monitored in the endophytic cells by using total RNA extracted from B501gfp1-inoculated wild rice plants during daily light-dark cycles. The level of nifH transcription in planta varied dramatically, with a maximum during the light period. Moreover, the light radiation enhanced nifH expression even in free-living cells grown in culture. These results suggest that in planta nitrogen fixation by the endophyte shows a daily rhythm determined by the plant's light environment.

Clostridium pasteurianum W5 synthesizes two NifH-related polypeptides under nitrogen-fixing conditions

Previous studies identified fivenifH-like genes (nifH2throughnifH6) inClostridium pasteurianum(strain W5), where thenifH1gene encodes the nitrogenase iron protein. Transcripts of thesenifHgenes, with the exception ofnifH3, were detected in molybdenum-sufficient nitrogen-fixing cells. However, the size of the transcripts, the level of transcription and the presence of polypeptides encoded by thenifH-like genes were not reported. ThenifH2andnifH6genes were extremely similar, as they seemed to differ by only two bases in a span of 2481 bp, one in the coding region and another in the upstream region. Re-examination of the DNA sequences revealed that the coding region ofnifH2andnifH6was identical, whereas the difference in the upstream region was confirmed. Results from the authors' ongoing study of thenifgenes of single-colony isolates ofC. pasteurianumsuggest that thenifH6designation should be eliminated. Here the size of mRNA fromnifH2and the detection of the NifH2 polypeptide in nitrogen-fixing cells ofC. pasteurianumare reported. Northern blot analysis of periodically collected nitrogen-fixing cells showed that thenifH1andnifH2mRNAs were present throughout growth. Addition of ammonium acetate repressed the transcription of both these genes similarly. Using an antiserum raised against NifH ofAzotobacter vinelandii, two NifH-related bands were detected by Western blot analysis after electrophoretic separation of proteins in extracts of nitrogen-fixingC. pasteurianumcells. After separation of proteins by preparative SDS-PAGE, the NifH polypeptides were characterized by MALDI-TOF-MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) and by ES-MS/MS (electrospray tandem mass spectrometry) analyses. The results confirmed the presence of NifH2, in addition to NifH1, in nitrogen-fixingC. pasteurianumcells.

Bacteremia caused by Clostridium intestinale

We describe a case of Clostridium intestinale bacteremia in a previously healthy adolescent female presenting with fever and abdominal pain. The bacterium was definitively identified via 16S rRNA gene sequencing. This is the first report, in the world literature, of human infection caused by this microorganism.