Not just passengers, but co-pilots! Non-rhizobial nodule-associated bacteria promote cowpea growth and symbiosis with (brady)rhizobia.

AIMS: To isolate and characterize non-rhizobial nodule-associated bacteria (NAB) from cowpea root-nodules regarding their performance of plant-growth-promoting mechanisms and their ability to enhance cowpea growth and symbiosis when co-inoculated with bradyrhizobia. METHODS AND RESULTS: Sixteen NAB were isolated, identified, and in vitro evaluated for plant growth promotion traits. The ability to promote cowpea growth was analyzed when co-inoculated with Bradyrhizobium pachyrhizi BR 3262 in sterile and non-sterile substrates. The 16S rRNA gene sequences analysis revealed that NAB belonged to the genera Chryseobacterium (4), Bacillus (3), Microbacterium (3), Agrobacterium (1), Escherichia (1), Delftia (1), Pelomonas (1), Sphingomonas (1), and Staphylococcus (1). All strains produced different amounts of auxin siderophores and formed biofilms. Twelve out of the 16 strains carried the nifH, a gene associated with nitrogen fixation. Co-inoculation of NAB (ESA 424 and ESA 29) with Bradyrhizobium pachyrhizi BR 3262 significantly promoted cowpea growth, especially after simultaneous inoculation with the three strains. CONCLUSIONS: NAB are efficient cowpea growth promoters and can improve the efficiency of the symbiosis between cowpea and the N2-fixing microsymbiont B. pachyrhizi BR 3262, mainly under a specific triple microbial association.

pH as a Driver for Ammonia-Oxidizing Archaea in Forest Soils.

In this study, we investigated the impact of soil pH on the diversity and abundance of archaeal ammonia oxidizers in 27 different forest soils across Germany. DNA was extracted from topsoil samples, the amoA gene, encoding ammonia monooxygenase, was amplified; and the amplicons were sequenced using a 454-based pyrosequencing approach. As expected, the ratio of archaeal (AOA) to bacterial (AOB) ammonia oxidizers' amoA genes increased sharply with decreasing soil pH. The diversity of AOA differed significantly between sites with ultra-acidic soil pH (<3.5) and sites with higher pH values. The major OTUs from soil samples with low pH could be detected at each site with a soil pH <3.5 but not at sites with pH >4.5, regardless of geographic position and vegetation. These OTUs could be related to the Nitrosotalea group 1.1 and the Nitrososphaera subcluster 7.2, respectively, and showed significant similarities to OTUs described from other acidic environments. Conversely, none of the major OTUs typical of sites with a soil pH >4.6 could be found in the ultra- and extreme acidic soils. Based on a comparison with the amoA gene sequence data from a previous study performed on agricultural soils, we could clearly show that the development of AOA communities in soils with ultra-acidic pH (<3.5) is mainly triggered by soil pH and is not influenced significantly by the type of land use, the soil type, or the geographic position of the site, which was observed for sites with acido-neutral soil pH.

Calling for a systems approach in microbiome research and innovation.

Microbiomes are all around us in natural and cultivated ecosystems, for example, soils, plants, animals and our own body. Microbiomes are essential players of biotechnological applications, and their functions drive human, animal, plant and environmental health. The rapidly developing microbiome research landscape was studied by a global mapping excercise and bibliometric analysis. Although microbiome research is performed in many different science fields, using similar concepts within and across fields, microbiomes are mostly investigated one ecosystem at-a-time. In order to fully understand microbiome impacts and leverage microbial functions, research needs to adopt a systems approach connecting microbiomes and research initiatives in divergent fields to create understanding on how microbiomes can be modulated for desirable functions as a basis of sustainable, circular bioeconomy.

Correction to: Microbiome definition re-visited: old concepts and new challenges.

An amendment to this paper has been published and can be accessed via the original article.

Microbiome definition re-visited: old concepts and new challenges.

The field of microbiome research has evolved rapidly over the past few decades and has become a topic of great scientific and public interest. As a result of this rapid growth in interest covering different fields, we are lacking a clear commonly agreed definition of the term "microbiome." Moreover, a consensus on best practices in microbiome research is missing. Recently, a panel of international experts discussed the current gaps in the frame of the European-funded MicrobiomeSupport project. The meeting brought together about 40 leaders from diverse microbiome areas, while more than a hundred experts from all over the world took part in an online survey accompanying the workshop. This article excerpts the outcomes of the workshop and the corresponding online survey embedded in a short historical introduction and future outlook. We propose a definition of microbiome based on the compact, clear, and comprehensive description of the term provided by Whipps et al. in 1988, amended with a set of novel recommendations considering the latest technological developments and research findings. We clearly separate the terms microbiome and microbiota and provide a comprehensive discussion considering the composition of microbiota, the heterogeneity and dynamics of microbiomes in time and space, the stability and resilience of microbial networks, the definition of core microbiomes, and functionally relevant keystone species as well as co-evolutionary principles of microbe-host and inter-species interactions within the microbiome. These broad definitions together with the suggested unifying concepts will help to improve standardization of microbiome studies in the future, and could be the starting point for an integrated assessment of data resulting in a more rapid transfer of knowledge from basic science into practice. Furthermore, microbiome standards are important for solving new challenges associated with anthropogenic-driven changes in the field of planetary health, for which the understanding of microbiomes might play a key role. Video Abstract.

Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges - A review.

Analyses of the spatial localization and the functions of bacteria in host plant habitats through in situ identification by immunological and molecular genetic techniques combined with high resolving microscopic tools and 3D-image analysis contributed substantially to a better understanding of the functional interplay of the microbiota in plants. Among the molecular genetic methods, 16S-rRNA genes were of central importance to reconstruct the phylogeny of newly isolated bacteria and to localize them in situ. However, they usually do not allow resolution for phylogenetic affiliations below genus level. Especially, the separation of opportunistic human pathogens from plant beneficial strains, currently allocated to the same species, needs genome-based resolving techniques. Whole bacterial genome sequences allow to discriminate phylogenetically closely related strains. In addition, complete genome sequences enable strain-specific monitoring for biotechnologically relevant strains. In this mini-review we present high resolving approaches for analysis of the composition and key functions of plant microbiota, focusing on interactions of diazotrophic plant growth promoting bacteria, like Azospirillum brasilense, with non-legume host plants. Combining high resolving microscopic analyses with specific immunological detection methods and molecular genetic tools, including especially transcriptome analyses of both the bacterial and plant partners, enables new insights into key traits of beneficial bacteria-plant interactions in holobiontic systems.

De Novo Genome Assembly of a Plant-Associated Rhodococcus qingshengii Strain (RL1) Isolated from Eruca sativa Mill. and Showing Plant Growth-Promoting Properties.

Rhodococcus qingshengii RL1 was isolated from surface-sterilized leaves of Eruca sativa Mill. and shows plant growth-promoting (PGP) properties. The de novo genome assembly consists of one chromosome with 6,253,838 bp and two plasmids with 144,038 bp and 448,745 bp. Many genes could be identified reflecting its PGP potential.

Distinct communities of Cercozoa at different soil depths in a temperate agricultural field.

Protists are the most important predators of soil microbes like bacteria and fungi and are highly diverse in terrestrial ecosystems. However, the structure of protistan communities throughout the soil profile is still poorly explored. Here, we used Illumina sequencing to track differences in the relative abundance and diversity of Cercozoa, a major group of protists, at two depths; 10-30 cm (topsoil) and 60-75 cm (subsoil) in an agricultural field in Germany. At the two depths, we also distinguished among three soil compartments: rhizosphere, drilosphere (earthworm burrows) and bulk soil. With increasing depth, we found an overall decline in richness, but we were able to detect subsoil specific phylotypes and contrasting relative abundance patterns between topsoil and subsoil for different clades. We also found that the compartment effect disappeared in the subsoil when compared to the topsoil. More studies are now needed to describe and isolate these possibly subsoil specific phylotypes and better understand their ecology and function.

Short-term dynamics of bacterial communities in a tidally affected coastal ecosystem.

Tidal effects on the composition of free-living (FL) and particle-associated (PA) bacterial communities were studied in a tidal flat ecosystem in the southern North Sea. Denaturing gradient gel electrophoresis targeting the 16S rRNA gene and the 16S rRNA of Bacteria, Bacteroidetes, Alphaproteobacteria and the Roseobacter clade was applied. Despite strong tidal variations in the quantity and, depending on the season, also the quality of suspended matter as well as variations in bacterial activity, the bacterial community composition remained rather stable. FISH showed some variations of the community composition, but these were not related to typical tidal situations. Variations were higher during tidal cycles in May and July compared with November. Bacteroidetes, Alpha- and Gammaproteobacteria constituted the majority of the bacterial communities but relative proportions of the different groups varied considerably. On particles, Betaproteobacteria were also detected to substantial proportions. The Roseobacter clade constituted up to 90% of FL but only 30% of PA Alphaproteobacteria. Banding patterns of the Bacteroidetes-specific amplicons, and in particular those targeting the 16S rRNA, revealed tidally induced effects, as several bands appeared or disappeared at distinct events such as slack water or resuspension. Sequencing of prominent bands revealed predominantly phylotypes reported previously from this ecosystem.

Bacteria utilizing plant-derived carbon in the rhizosphere of Triticum aestivum change in different depths of an arable soil.

Root exudates shape microbial communities at the plant-soil interface. Here we compared bacterial communities that utilize plant-derived carbon in the rhizosphere of wheat in different soil depths, including topsoil, as well as two subsoil layers up to 1 m depth. The experiment was performed in a greenhouse using soil monoliths with intact soil structure taken from an agricultural field. To identify bacteria utilizing plant-derived carbon, 13 C-CO2 labelling of plants was performed for two weeks at the EC50 stage, followed by isopycnic density gradient centrifugation of extracted DNA from the rhizosphere combined with 16S rRNA gene-based amplicon sequencing. Our findings suggest substantially different bacterial key players and interaction mechanisms between plants and bacteria utilizing plant-derived carbon in the rhizosphere of subsoils and topsoil. Among the three soil depths, clear differences were found in 13 C enrichment pattern across abundant operational taxonomic units (OTUs). Whereas, OTUs linked to Proteobacteria were enriched in 13 C mainly in the topsoil, in both subsoil layers OTUs related to Cohnella, Paenibacillus, Flavobacterium showed a clear 13 C signal, indicating an important, so far overseen role of Firmicutes and Bacteriodetes in the subsoil rhizosphere.

Cowpea Nodules Harbor Non-rhizobial Bacterial Communities that Are Shaped by Soil Type Rather than Plant Genotype.

Many studies have been pointing to a high diversity of bacteria associated to legume root nodules. Even though most of these bacteria do not form nodules with legumes themselves, it was shown that they might enter infection threads when co-inoculated with rhizobial strains. The aim of this work was to describe the diversity of bacterial communities associated with cowpea (Vigna unguiculata L. Walp) root nodules using 16S rRNA gene amplicon sequencing, regarding the factors plant genotype and soil type. As expected, Bradyrhizobium was the most abundant genus of the detected genera. Furthermore, we found a high bacterial diversity associated to cowpea nodules; OTUs related to the genera Enterobacter, Chryseobacterium, Sphingobacterium, and unclassified Enterobacteriacea were the most abundant. The presence of these groups was significantly influenced by the soil type and, to a lesser extent, plant genotype. Interestingly, OTUs assigned to Chryseobacterium were highly abundant, particularly in samples obtained from an Ultisol soil. We confirmed their presence in root nodules and assessed their diversity using a target isolation approach. Though their functional role still needs to be addressed, we postulate that Chryseobacterium strains might help cowpea plant to cope with salt stress in semi-arid regions.

Prokaryotes in Subsoil-Evidence for a Strong Spatial Separation of Different Phyla by Analysing Co-occurrence Networks.

Microbial communities in soil provide a wide range of ecosystem services. On the small scale, nutrient rich hotspots in soil developed from the activities of animals or plants are important drivers for the composition of microbial communities and their functional patterns. However, in subsoil, the spatial heterogeneity of microbes with differing lifestyles has been rarely considered so far. In this study, the phylogenetic composition of the bacterial and archaeal microbiome based on 16S rRNA gene pyrosequencing was investigated in the soil compartments bulk soil, drilosphere, and rhizosphere in top- and in the subsoil of an agricultural field. With co-occurrence network analysis, the spatial separation of typically oligotrophic and copiotrophic microbes was assessed. Four bacterial clusters were identified and attributed to bulk topsoil, bulk subsoil, drilosphere, and rhizosphere. The bacterial phyla Proteobacteria and Bacteroidetes, representing mostly copiotrophic bacteria, were affiliated mainly to the rhizosphere and drilosphere-both in topsoil and subsoil. Acidobacteria, Actinobacteria, Gemmatimonadetes, Planctomycetes, and Verrucomicrobia, bacterial phyla which harbor many oligotrophic bacteria, were the most abundant groups in bulk subsoil. The bacterial core microbiome in this soil was estimated to cover 7.6% of the bacterial sequencing reads including both oligotrophic and copiotrophic bacteria. In contrast the archaeal core microbiome includes 56% of the overall archaeal diversity. Thus, the spatial variability of nutrient quality and quantity strongly shapes the bacterial community composition and their interaction in subsoil, whereas archaea build a stable backbone of the soil prokaryotes due to their low variability in the different soil compartments.

Colonization of plants by human pathogenic bacteria in the course of organic vegetable production.

In recent years, increasing numbers of outbreaks caused by the consumption of vegetables contaminated with human pathogenic bacteria were reported. The application of organic fertilizers during vegetable production is one of the possible reasons for contamination with those pathogens. In this study laboratory experiments in axenic and soil systems following common practices in organic farming were conducted to identify the minimal dose needed for bacterial colonization of plants and to identify possible factors like bacterial species or serovariation, plant species or organic fertilizer types used, influencing the success of plant colonization by human pathogenic bacteria. Spinach and corn salad were chosen as model plants and were inoculated with different concentrations of Salmonella enterica sv. Weltevreden, Listeria monocytogenes sv. 4b and EGD-E sv. 1/2a either directly (axenic system) or via agricultural soil amended with spiked organic fertilizers (soil system). In addition to PCR- and culture-based detection methods, fluorescence in situ hybridization (FISH) was applied in order to localize bacteria on or in plant tissues. Our results demonstrate that shoots were colonized by the pathogenic bacteria at inoculation doses as low as 4 × 10 CFU/ml in the axenic system or 4 × 10(5) CFU/g in the soil system. In addition, plant species dependent effects were observed. Spinach was colonized more often and at lower inoculation doses compared to corn salad. Differential colonization sites on roots, depending on the plant species could be detected using FISH-CLSM analysis. Furthermore, the transfer of pathogenic bacteria to plants via organic fertilizers was observed more often and at lower initial inoculation doses when fertilization was performed with inoculated slurry compared to inoculated manure. Finally, it could be shown that by introducing a simple washing step, the bacterial contamination was reduced in most cases or even was removed completely in some cases.

Endophytic Bradyrhizobium spp. isolates from sugarcane obtained through different culture strategies.

Brazilian sugarcane has been shown to obtain part of its nitrogen via biological nitrogen fixation (BNF). Recent reports, based on the culture independent sequencing of bacterial nifH complementary DNA (cDNA) from sugarcane tissues, have suggested that members of the Bradyrhizobium genus could play a role in sugarcane-associated BNF. Here we report on the isolation of Bradyrhizobium spp. isolates and a few other species from roots of sugarcane cultivar RB867515 by two cultivation strategies: direct isolation on culture media and capture of Bradyrhizobium spp. using the promiscuous legume Vigna unguiculata as trap-plant. Both strategies permitted the isolation of genetically diverse Bradyrhizobium spp. isolates, as concluded from enterobacterial repetitive intergenic consensus polymerase chain reaction (PCR) fingerprinting and 16S ribosomal RNA, nifH and nodC sequence analyses. Several isolates presented nifH phylotypes highly similar to nifH cDNA phylotypes detected in field-grown sugarcane by a culture-independent approach. Four isolates obtained by direct plate cultivation were unable to nodulate V. unguiculata and, based on PCR analysis, lacked a nodC gene homologue. Acetylene reduction assay showed in vitro nitrogenase activity for some Bradyrhizobium spp. isolates, suggesting that these bacteria do not require a nodule environment for BNF. Therefore, this study brings further evidence that Bradyrhizobium spp. may play a role in sugarcane-associated BNF under field conditions.

Influence of non-invasive X-ray computed tomography (XRCT) on the microbial community structure and function in soil.

In this study the influence of X-ray computed tomography (XRCT) on the microbial community structure and function in soils has been investigated. Our results clearly indicate that XRCT of soil samples has a strong impact on microbial communities and changes structure and function significantly due to the death of selected microbial groups as a result of the treatment.

Biogeography and phylogenetic diversity of a cluster of exclusively marine myxobacteria.

Myxobacteria are common in terrestrial habitats and well known for their formation of fruiting bodies and production of secondary metabolites. We studied a cluster of myxobacteria consisting only of sequences of marine origin (marine myxobacteria cluster, MMC) in sediments of the North Sea. Using a specific PCR, MMC sequences were detected in North Sea sediments down to 2.2 m depth, but not in the limnetic section of the Weser estuary and other freshwater habitats. In the water column, this cluster was only detected on aggregates up to a few meters above the sediment surface, but never in the fraction of free-living bacteria. A quantitative real-time PCR approach revealed that the MMC constituted up to 13% of total bacterial 16S rRNA genes in surface sediments of the North Sea. In a global survey, including sediments from the Mediterranean Sea, the Atlantic, Pacific and Indian Ocean and various climatic regions, the MMC was detected in most samples and to a water depth of 4300 m. Two fosmids of a library from sediment of the southern North Sea containing 16S rRNA genes affiliated with the MMC were sequenced. Both fosmids have a single unlinked 16S rRNA gene and no complete rRNA operon as found in most bacteria. No synteny to other myxobacterial genomes was found. The highest numbers of orthologues for both fosmids were assigned to Sorangium cellulosum and Haliangium ochraceum. Our results show that the MMC is an important and widely distributed but largely unknown component of marine sediment-associated bacterial communities.

Improved protocol for the simultaneous extraction and column-based separation of DNA and RNA from different soils.

We developed an improved protocol, allowing the simultaneous extraction of DNA and RNA from soil using phenol-chloroform with subsequent column-based separation of DNA and RNA (PCS). We compared this new approach with the well established protocol published by Griffiths et al. (2000), where DNA and RNA are separated by selective enzymatic digestions and two commercial kits used for DNA or RNA extraction, respectively, using four different agricultural soils. We compared yield and purity of the nucleic acids as well as abundance and diversity profiles of the soil bacterial communities targeting the nosZ gene via quantitative real-time PCR and terminal restriction fragment length polymorphism on DNA and RNA level. The newly developed protocol provided purer nucleic acid extracts compared to the used kit-based protocols. All protocols were suitable for DNA- and RNA-based gene quantification, however high variations between replicates were obtained for RNA samples using the original Griffiths protocol. Diversity patterns of nosZ were highly influenced by the extraction protocol used both on the DNA and RNA level. Finally, our data showed that the new protocol allows a simultaneous and reproducible extraction and separation of DNA and RNA, which were suitable for reliable analyses of gene and transcript copy numbers and diversity pattern.

Dynamic regulation of N-acyl-homoserine lactone production and degradation in Pseudomonas putida IsoF.

The biocontrol strain Pseudomonas putida IsoF, which was isolated from a tomato rhizosphere, is a known N-acyl-homoserine lactone (AHL) producer with only one LuxI/LuxR-like quorum-sensing (QS) system. The production and degradation of AHLs were analysed in different growth phases of the bacterium. Using the analytical tools of ultra performance liquid chromatography and high resolution MS, it was possible to determine not only the various AHLs synthesized over time but also their degradation products. 3-oxo-decanoyl-homoserine lactone was found to be the dominant AHL, which reached its maximum in the early logarithmic growth phase. Although the pH of the medium was neutral, the AHLs were degraded thereafter rapidly to the corresponding homoserines and other metabolites. The proposed lactonase gene of P. putida IsoF could not be identified, because it is apparently quite different from hitherto described lactonases. The analytical data were used to calculate the rates and thresholds of AHL production by mathematical modelling, allowing quantitative predictions and a further understanding of the QS-based regulations in this bacterium. This study, combining microbiological, chemical and mathematical approaches, suggests that AHL degradation is an integral part of the whole autoinducer circuit of P. putida IsoF.