Bulk Soil Bacterial Communities Research Articles

Host ancestry and morphology differentially influence bacterial and fungal community structure of Rhododendron leaves, roots, and soil

Rhododendron are popular ornamental plants that are well-known for forming mycorrhizal associations with ericoid fungi, but little is known about how host traits influence their microbiome more broadly. This study investigated leaf, root, rhizosphere soil, and bulk soil bacterial and fungal community structure for 12 Rhododendron species, representing four taxonomic clades with different leaf habits. Samples were collected when ephemeral hair roots colonized by ericoid mycorrhizae were absent, and microbial community structure was compared to leaf and root morphology for the same plants. Root morphology and the fungal communities of roots and rhizosphere soil were primarily structured by host ancestry. Leaf bacterial and fungal communities were even more distinct across clades than for roots or rhizosphere, and microbial communities of leaves and bulk soil were similarly structured by clade-wise differences in leaf morphology, suggesting a role for Rhododendron leaf litter in belowground microbial community structure. This work sheds new light on host traits influencing microbial community structure of ericaceous plants, showing a strong influence of ancestry, but also that different host traits drive bacterial and fungal communities across different plant compartments, suggesting future work on factors that drive similarity among close relatives in the non-ericoid microbes associating with Rhododendron.

Pulse Frequency in Crop Rotations Alters Soil Microbial Community Networks and the Relative Abundance of Fungal Plant Pathogens.

Including pulse crops in cereal-based cropping systems has become a widely accepted and useful agronomic practice to increase crop diversification and biologically fixed nitrogen in agroecosystems. However, there is a lack of knowledge regarding how the intensification of pulses in crop rotations influence soil microbial communities. In this study, we used an amplicon sequencing approach to examine the bulk and rhizosphere soil bacterial and fungal communities from the wheat (Triticum aestivum L.) phase (final year of 4 years rotations) of a long-term pulse intensification field trial in the semi-arid region of the Canadian Prairies. Our results revealed pulse frequency had a minimal impact on microbial α-diversity, but caused a significant shift in the composition of the fungal (rhizosphere and bulk soil) and bacterial (bulk soil) communities. This effect was the most pronounced in the Ascomycete and Bacteroidete communities. Increasing pulse frequency also promoted a higher proportion of fungal pathotrophs in the bulk soil, particularly those putatively identified as plant pathogens. The network analysis revealed that rotations with higher pulse frequency promoted increased competition within the soil microbial networks in the rhizosphere and bulk soil. However, we also detected more negative interactions among the dominant pathotrophic taxa with increased pulse frequency, suggesting higher soil-borne disease potential. These findings highlight the potential drawbacks and reduced sustainability of increasing pulse frequency in crop rotations in semiarid environments.

Different crop rotation systems change the rhizosphere bacterial community structure of Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao

Continuous cropping obstacles often lead to a decline in the quality and yield of traditional Chinese medicine plants. Crop rotation effectively alleviates the obstacles of continuous cropping. However, there are few studies on the rotation of traditional Chinese medicine crops. Astragalus membranaceus (Fisch) Bge. var. mongholicus (Bge.) Hsiao (A. mongholicus) is a commonly used traditional Chinese medicine. The present study investigates the growth of A. mongholicus and its associated soil microbiome and physicochemical properties under different crop rotation regimes in a field and pot experiment. The 16S rRNA gene high throughput sequencing was used to compare the composition and diversity of rhizosphere, bulk soil and endosphere bacterial communities of A. mongholicus after 5 years of crop rotation. Crop rotation with Avena sativa L, significantly increased the growth of A. mongholicus and elevated soil organic matter, total nitrogen, total phosphorus and available potassium contents. Crop rotation increased the bacterial community diversity in the rhizosphere of A. mongholicus and abundance of some beneficial bacteria, such as Clostridia, Rubrobacterales and Micromonosporales. The composition of the rhizosphere bacterial community differed between sampling times and depending on crop rotation. Briefly, crop rotation with Avena sativa L was beneficial to soil quality and A. mongholicus growth, and it is a good option to alleviate A. mongholicus continuous cropping obstacles.

Bacterial communities associated with natural and commercially grown rooibos (Aspalathus linearis)

Aspalathus linearis is a commercially important plant species endemic to the Cape Floristic Region of South Africa and is used to produce a herbal tea known as rooibos tea. Symbiotic interactions between A. linearis and soil bacteria play an important role in the survival of Aspalathus plants in the highly nutrient-poor, acidic fynbos soil. The aim of this study was to characterize and compare rhizosphere and bulk soil bacterial communities associated with natural and commercially grown A. linearis, as well as the effect of seasonal changes on these communities. Bacterial communities were characterized using high throughput amplicon sequencing, and their correlations with soil chemical properties were investigated. The N-fixing bacterial community was characterized using terminal restriction fragment length polymorphism and real time quantitative polymerase chain reaction. Actinobacteria, Proteobacteria, and Acidobacteria were the most dominant bacterial phyla detected in this study. Highly similar bacterial communities were associated with natural and commercially grown plants. Significant differences in the bacterial community were observed between rhizosphere and bulk soils collected in the dry season, while no significant differences were detected in the wet season. This study provides insights into bacterial community structure and potential factors shaping bacterial community structure with commercially important A. linearis.

Effects of Drought-Tolerant Ea-DREB2B Transgenic Sugarcane on Bacterial Communities in Soil.

Drought is a major abiotic stress affecting plant growth and development. Sugarcane, a sugar crop planted in warmer climate, suffers dramatically from drought stress. Bacterial communities colonizing the rhizosphere, where roots sense drought stress initially, have been well studied for their beneficial effects on plant growth and health. The Ea-DREB2B gene cloned from the sugarcane, Saccharum arundinaceum, belongs to the DREB2 subgroup of the DREB gene family, which is involved in drought response regulation. Here, we present a detailed characterization of the rhizoplane, rhizosphere, and bulk soil bacterial communities determined using a high-sequencing approach with the transgenic (TG) sugarcane variety GN18 harboring the drought-tolerant Ea-DREB2B gene and its isogenic wild-type (WT) variety FN95-1702 under the same environmental conditions. In addition, the total carbon (TC), total nitrogen (TN), and total phosphorus (TP) contents in each soil area were compared to explore the relationship between bacterial alteration in the TG and WT plants and environmental factors (TC, TN, TP, C:N, C:P, and N:P). Our results showed that the bacterial communities in the rhizosphere and rhizoplane of TG sugarcane were more similar and perfectly correlated with the environmental factors than those of the WT. This suggested that the bacterial communities of the TG plants were altered in response to the changes in root exudates. The results of our study suggest that the change in soil environment caused by transgenic sugarcane alters soil bacterial communities.

Crop rotation, but not cover crops, influenced soil bacterial community composition in a corn-soybean system in southern Wisconsin

Crop rotation, the successive cultivation of different crops on the same field, has been practiced for centuries, and it is often associated with increased crop yields. Cover cropping is a less ubiquitous farming practice that also increases plant biodiversity over time. Cover crops are a soil conservation tool; they are grown between harvest and planting of the main crop to protect and enrich the soil. Increasing crop diversity with crop rotation and cover cropping may contribute to shifts in soil bacterial communities. Our first objective was to investigate the soil bacterial communities associated with growing corn (Zea mays L.) or soybean (Glycine max L.) continuously versus annually rotating these crops. Our second objective was to determine if the first season of cover cropping had an impact on soil bacteria in a corn-soybean system. Soil was collected from a long-term crop rotational study with continuous corn, continuous soybean, and annually rotated corn-soybean treatments. These rotation treatments had various cover crops established within each plot, which were sampled individually. Bacterial communities were estimated in each sample by extracting DNA and sequencing the V3-V4 region of the 16S rRNA gene. We found that soil pH, organic matter, and certain macronutrients were essential drivers in determining the composition of bulk soil bacterial communities. Continuously cropped corn and soybean had distinct bacterial communities, while annually rotated communities were similar in both crop phases. The incorporation of cover crops into the rotation system did not result in significant changes to the bulk soil bacterial community. This result was probably due to limited cover crop growth in the first year of establishment, and a limited amount of time for soil communities to respond to this change.

Application sequence modulates microbiome composition, plant growth and apple replant disease control efficiency upon integration of anaerobic soil disinfestation and mustard seed meal amendment

Anaerobic soil disinfestation (ASD) and mustard seed meal (MSM) amendments can provide effective control of soil-borne diseases including apple replant disease. These measures rely on both chemical and biological modes of action to yield effective disease control and their integration may prove beneficial or, alternatively, deleterious to overall treatment efficiency when applied in concert. Potential outcomes of integrating ASD with MSM amendments were assessed by determining the effect of treatment application sequence and ASD carbon source on generation of allyl isothiocyanate (AITC) derived from Brassica juncea seed meal, structure of the rhizosphere and soil microbiome, control of apple replant pathogens, and plant growth. In bioassays conducted using ‘Gala’ apple seedlings, application of ASD or MSM treatments independently was as effective or superior to all integrated treatments for the control of replant pathogens. Application of ASD prior to MSM amendment diminished the yield of AITC attained in response to soil incorporation of the Brassica juncea:Sinapis alba seed meal. Treatment application sequence had significant effect on structure of the bulk soil fungal and bacterial community. Correspondingly, treatment application sequence significantly altered plant growth performance when orchard grass was utilized as the ASD carbon input. At harvest, rhizosphere fungal but not bacterial community composition was significantly altered in treated soil relative to the control, and sequence of treatment application had significant effect on rhizosphere fungal community structure. Failure of integrated treatments to enhance overall replant disease control may have resulted from many factors including reduced generation of active metabolites, diminished activity of mechanisms functional in pathogen suppression, or the elevated accumulation and retention of phytotoxic chemistries, the latter which would require extended plant back periods to circumvent. The findings indicate that under the experimental conditions employed, integration of ASD with MSM amendment is unlikely to yield additive or synergistic effects on apple replant disease control.

Development of microbial communities in organochlorine pesticide contaminated soil: A post-reclamation perspective

In order to meet constantly increasing demands for land without damaging pristine environments like forests or grasslands, reclamation and re-purposing of historically contaminated areas should become a priority. Successful reclamation goes hand in hand with the soil functional recovery potential and with resilient microbial communities capable of performing the necessary ecosystem services. In this context, we designed a greenhouse pot experiment as a mock reclamation situation, where traces of lindane at hazard threshold and twice the concentration accepted for waste deposits are left in the soil after conventional clean-up by excavation and land filling. We assessed the effects of lindane at 50 and 100 mg kg−1 regarding crop growth and nutrient turnover (with focus on the nitrogen cycle) as two key parameters for soil functions. The bulk and rhizosphere soil bacterial community composition were chosen as parameters for soil resilience in lindane contamination conditions. Lindane severely affected plant growth and development. The potential nitrogen fixation, quantified as nifH gene copy number, suffered direct negative effects of lindane contamination in bulk soil, which could represent an additional obstacle for phytoremediation. Changes in rhizosphere bacterial community composition were related to lindane toxic effects towards the plants, which might have supported the growth of opportunists and saprophytes. In bulk soil, the bacterial community shifted towards lindane tolerant taxa like Sphingomonas and Porphyrobacter that are interesting with regard to their applications in bioremediation. We concluded that lindane at hazard threshold concentration left in soil after clean-up has negative effects both soil functionality, and the recovery of the bacterial communities to their original composition when lindane resistant plant crops are not involved.

Assessment of species richness and diversity ofPrunus aviumrhizosphere and bulk soil bacterial communities

Microorganisms play an important role in mediating interactions in plant-soil rhizospheres. Cherry roots generally have poor adaptability and are sensitive to soil environment changes; as such, the microbial community structure and soil biological activity largely determine the nature of cherry root physiological functions and morphogenesis. To determine the impact of seasons and the presence of cherry roots on the abundance and structure of bacterial communities in soil, we investigated the bacterial communities colonizing the cherry rhizosphere and non-rhizosphere (bulk soil) during three growing seasons using Illumina high-throughput sequencing of the 16S rRNA gene hypervariable region. In all, 3,627 operational taxonomic units (OTUs) belonging to 58 genera and seven unclassified phyla were identified and assigned to 27 broad taxonomic groups. The bacterial communities were dominated by members of Proteobacteria, followed by those of Acidobacteria and Actinobacteria. The largest number of OTUs was observed in summer. More diverse bacterial communities were observed in the bulk soil than in the rhizosphere; however, the bulk soil generally had a lower abundance of each species. Different functional bacteria could be identified in the rhizosphere and non-rhizosphere, suggesting that cherry roots quantitatively and qualitatively influenced soil bacterial communities of cherry orchards. This study enhances our understanding of the soil niche effect on bacterial diversity in orchards and validates the effectiveness of high-throughput sequencing in surveying soil microbial diversity.

Plant genus (Acacia and Eucalyptus) alters soil microbial community structure and relative abundance within revegetated shelterbelts

The composition of native woody vegetation communities in restored agricultural landscapes can alter plant-soil interactions and thus ecological function. This study investigated the effects of primary species groups (Acacia, Eucalyptus) used in shelterbelts in south-eastern Australia on soil microbial community structure, compared with those under adjacent pastures. The quantity and structure of bacterial and fungal communities was analysed using quantitative PCR (qPCR) and terminal restriction fragment length polymorphism (TRFLP). The fungal:bacterial ratio was highest under Eucalyptus trees but did not differ between Acacia and pasture. Both fungal and bacterial communities varied at different depths in the soil profile and across sampling periods. The dominant tree genus was a significant factor in observed differences in bulk soil bacterial and fungal communities compared to the surrounding pasture. The effect of tree type on fungal communities was more pronounced than on bacterial communities. Fungal communities not only differed between shelterbelts and pastures, but also between Acacia and Eucalyptus dominated shelterbelts; these patterns were consistently observed at different soil depths. Shelterbelt systems which contain a mixture of different plant genera have the potential to exhibit greater microbial community heterogeneity than single species plantations. Maintaining a variety of tree species during afforestation may therefore contribute to conserving important bacterial and fungal diversity in agricultural landscapes.

Root exudates drive the soil-borne legacy of aboveground pathogen infection

BackgroundPlants are capable of building up beneficial rhizosphere communities as is evidenced by disease-suppressive soils. However, it is not known how and why soil bacterial communities are impacted by plant exposure to foliar pathogens and if such responses might improve plant performance in the presence of the pathogen. Here, we conditioned soil by growing multiple generations (five) of Arabidopsis thaliana inoculated aboveground with Pseudomonas syringae pv tomato (Pst) in the same soil. We then examined rhizosphere communities and plant performance in a subsequent generation (sixth) grown in pathogen-conditioned versus control-conditioned soil. Moreover, we assessed the role of altered root exudation profiles in shaping the root microbiome of infected plants.ResultsPlants grown in conditioned soil showed increased levels of jasmonic acid and improved disease resistance. Illumina Miseq 16S rRNA gene tag sequencing revealed that both rhizosphere and bulk soil bacterial communities were altered by Pst infection. Infected plants exhibited significantly higher exudation of amino acids, nucleotides, and long-chain organic acids (LCOAs) (C > 6) and lower exudation levels for sugars, alcohols, and short-chain organic acids (SCOAs) (C ≤ 6). Interestingly, addition of exogenous amino acids and LCOA also elicited a disease-suppressive response.ConclusionCollectively, our data suggest that plants can recruit beneficial rhizosphere communities via modification of plant exudation patterns in response to exposure to aboveground pathogens to the benefit of subsequent plant generations.

Rhizobacterial communities of five co-occurring desert halophytes.

BackgroundRecently, researches have begun to investigate the microbial communities associated with halophytes. Both rhizobacterial community composition and the environmental drivers of community assembly have been addressed. However, few studies have explored the structure of rhizobacterial communities associated with halophytic plants that are co-occurring in arid, salinized areas.MethodsFive halophytes were selected for study: these co-occurred in saline soils in the Ebinur Lake Nature Reserve, located at the western margin of the Gurbantunggut Desert of Northwestern China. Halophyte-associated bacterial communities were sampled, and the bacterial 16S rDNA V3–V4 region amplified and sequenced using the Illumina Miseq platform. The bacterial community diversity and structure were compared between the rhizosphere and bulk soils, as well as among the rhizosphere samples. The effects of plant species identity and soil properties on the bacterial communities were also analyzed.ResultsSignificant differences were observed between the rhizosphere and bulk soil bacterial communities. Diversity was higher in the rhizosphere than in the bulk soils. Abundant taxonomic groups (from phylum to genus) in the rhizosphere were much more diverse than in bulk soils. Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes and Planctomycetes were the most abundant phyla in the rhizosphere, while Proteobacteria and Firmicutes were common in bulk soils. Overall, the bacterial community composition were not significantly differentiated between the bulk soils of the five plants, but community diversity and structure differed significantly in the rhizosphere. The diversity of Halostachys caspica, Halocnemum strobilaceum and Kalidium foliatum associated bacterial communities was lower than that of Limonium gmelinii and Lycium ruthenicum communities. Furthermore, the composition of the bacterial communities of Halostachys caspica and Halocnemum strobilaceum was very different from those of Limonium gmelinii and Lycium ruthenicum. The diversity and community structure were influenced by soil EC, pH and nutrient content (TOC, SOM, TON and AP); of these, the effects of EC on bacterial community composition were less important than those of soil nutrients.DiscussionHalophytic plant species played an important role in shaping associated rhizosphere bacterial communities. When salinity levels were constant, soil nutrients emerged as key factors structuring bacterial communities, while EC played only a minor role. Pairwise differences among the rhizobacterial communities associated with different plant species were not significant, despite some evidence of differentiation. Further studies involving more halophyte species, and individuals per species, are necessary to elucidate plant species identity effects on the rhizosphere for co-occurring halophytes.

Bulk soil bacterial community structure and function respond to long-term organic and conventional agricultural management.

Understanding how soil microbiomes respond to management is essential to maximizing soil health. We contrasted microbiomes in bulk soil under long-term organic and conventional management in a grain production setting. Management category significantly impacted the relative abundances of 17% of the most abundant taxa. Both conventional and organic management favored particular taxa, but these effects were not reflected in summary richness and diversity indices. Management systems also lead to differences in soil edaphic properties, including pH and nutrient status; this may have been the mechanism by which change in the prokaryote community was enacted. Community change between years of sampling was less pronounced, with only 6 taxa differentially abundant among years. Management category also impacted the abundance of functional genes related to the production and consumption of greenhouse gases. Particulate methane monooxygenase genes were more frequent in soil under organic management, while soluble methane monooxygenase genes were more frequent in soil under conventional management in 1 of 2 years. Nitrous oxide reductase genes were significantly less abundant in soils under second-year alfalfa than in soils under corn. This work highlights the ability of agricultural management to enact broad rearrangements to the structure of bulk soil bacterial communities.

Responses of bacterial community to dibutyl phthalate pollution in a soil-vegetable ecosystem

Phthalate esters (PAEs) are a type of plasticizer that has aroused great concern due to their mutagenic, teratogenic, and carcinogenic effects, wherefore dibutyl phthalate (DBP) and other PAEs have been listed as priority pollutants. In this study, the impacts of DBP on a soil-vegetable ecosystem were investigated. The results showed that DBP could accumulate within vegetable tissues, and the accumulative effect was enhanced with higher levels of DBP contamination in soils. DBP accumulation also decreased vegetable quality in various ways, including decreased soluble protein content and increased nitrate content. The diversity of bacteria in soils gradually decreased with increasing DBP concentration, while no clear association with endophytic bacteria was observed. Also, the relative abundance, structure, and composition of soil bacterial communities underwent successional change during the DBP degradation period. The variation of bulk soil bacterial community was significantly associated with DBP concentration, while changes in the rhizosphere soil bacteria community were significantly associated with the properties of both soil and vegetables. The results indicated that DBP pollution could increase the health risk from vegetables and alter the biodiversity of indigenous bacteria in soil-vegetable ecosystems, which might further alter ecosystem functions in agricultural fields.

Arsenic mitigation in paddy soils by using microbial fuel cells

Arsenic (As) behavior in paddy soils couples with the redox process of iron (Fe) minerals. When soil is flooded, Fe oxides are transformed to soluble ferrous ions by accepting the electrons from Fe reducers. This process can significantly affect the fate of As in paddy fields. In this study, we show a novel technique to manipulate the Fe redox processes in paddy soils by deploying soil microbial fuel cells (sMFC). The results showed that the sMFC bioanode can significantly decrease the release of Fe and As into soil porewater. Iron and As contents around sMFC anode were 65.0% and 47.0% of the control respectively at day 50. The observed phenomenon would be explained by a competition for organic substrate between sMFC bioanode and the iron- and arsenic-reducing bacteria in the soils. In the vicinity of bioanode, organic matter removal efficiencies were 10.3% and 14.0% higher than the control for lost on ignition carbon and total organic carbon respectively. Sequencing of the 16S rRNA genes suggested that the influence of bioanodes on bulk soil bacterial community structure was minimal. Moreover, during the experiment a maximum current and power density of 0.31 mA and 12.0 mWm−2 were obtained, respectively. This study shows a novel way to limit the release of Fe and As in soils porewater and simultaneously generate electricity.

Long-term fertilization changes bacterial diversity and bacterial communities in the maize rhizosphere of Chinese Mollisols

The rhizosphere is a dynamic interface in which interactions among a myriad of microorganisms affect plants growth and tolerance to biotic and abiotic stress. Although rhizosphere effects on soil microbial communities have been widely investigated, few studies have evaluated such impacts of long-term fertilization on rhizosphere microbial communities in black soils common to northeast China. Here, we applied quantitative real-time polymerase chain reaction and high-throughput pyrosequencing to characterize rhizosphere and bulk soil bacterial communities in a long-term (36-year) fertilizer experiment. Soils were subjected to six treatments: CK (no fertilizer), N1 (150 kg urea ha−1 y−1), N2 (300 kg urea ha−1 y−1), M (18,600 kg horse manure ha−1 y−1), NPK (150 kg urea plus 33 kg P plus 62 kg K ha−1 y−1), and MNPK (M plus NPK). Inorganic fertilizer, especially N, decreased the 16S rRNA gene copy numbers and bacterial diversity in the rhizosphere and bulk soil, while manure fertilizer increased these values. Moreover, 16S rRNA gene copy numbers were higher and bacterial diversity was lower in the rhizosphere than the bulk soil, indicating that the maize rhizosphere had significant effects on bacterial diversity. The bacterial communities were predominantly composed of Proteobacteria and Acidobacteria in both the rhizosphere and bulk soil, but the rhizosphere and bulk soil communities were distinguished by principal coordinates analysis. Soil pH correlated with bacterial community composition and diversity in both rhizosphere and bulk soil. However, bacterial community composition in rhizosphere was more correlated with soil nutrient concentrations than in bulk soil under long-term fertilization. A redundancy analysis also indicated that soil pH, organic matter and available phosphorus concentrations were the most important factors in shaping bacterial communities in the maize rhizosphere. Our results revealed that long-term fertilization with increasing nutrients availability increased bacterial abundance, decreased biodiversity and changed bacterial composition in the rhizosphere.

Continuous application of different organic additives can suppress tomato disease by inducing the healthy rhizospheric microbiota through alterations to the bulk soil microflora

AimsBio-organic fertilizer and different additives are widely applied to suppress soil-borne diseases. However, how different additives alter bulk soil microflora and thereby induce the healthy rhizospheric microflora remains unclear.MethodsA 3-season field experiment containing four fertilization management programs (chemical fertilizer, organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer was conducted in a tomato production agroecosystem with high disease incidence to evaluate the induced efficacy. The bacterial and fungal microflora of bulk and rhizosphere soil influenced by different management programs were performed on the Illumina MiSeq platform. Principal coordinate analysis based on the Bray-Curtis distance metric was performed to compare the similarities and differences of the bacterial and fungal community compositions among all soil samples.ResultsSoil amended with organic fertilizer, amino acid organic fertilizer, and bio-organic fertilizer progressively and significantly suppressed tomato diseases in comparison with chemical fertilizer, and bio-organic fertilizer presented the best efficacy in all seasons. Interestingly, rhizospheric and bulk soil bacterial and fungal communities of the different fertilization management programs were separated from each other. Six bacterial and 10 fungal rhizospheric genera positively correlated with the same genera observed in bulk soil showing significant relationships with tomato disease incidence were observed, and functional strain SQR9 can be detected in the bulk and rhizosphere soils of bio-organic fertilizer treatments. Additionally, the redundancy analysis results showed the genera in treated chemical fertilizer bulk soil were dominated by Ralstonia and Fusarium, the abundances of which were highest and lowest in treated chemical fertilizer and bio-organic fertilizer rhizosphere, respectively.ConclusionsThis study provided insights into soil-borne disease suppression by bulk soil management and confirmed that alterations to the bulk soil microbiota by different organic additives played distinct roles in the formation of rhizospheric soil microflora for the suppression of disease.

Organic Amendments in a Long-term Field Trial-Consequences for the Bulk Soil Bacterial Community as Revealed by Network Analysis.

This study intended to elucidate the long-term effects of organic soil amendments on bacterial co-occurrence in bulk soil with and without addition of mineral fertiliser. Previous research mostly neglected the bacterial co-occurrence structure and focussed mainly on the parameters species diversity and abundance changes of species. Here we present a systematic comparison of two frequently used soil amendments, manure and straw, with regard to their impact on bacterial co-occurrence in a long-term field trial in Speyer, Germany. The approach involved 16S amplicon sequencing in combination with a bacterial network analysis, comparing the different fertiliser regimes. The results show an increase of bacterial diversity as well as an accumulation of bacteria of the order Bacillales in plots fertilised with manure compared to a control treatment. In the straw-amended plots neither an increase in diversity was found nor were indicative species detectable. Furthermore, network analysis revealed a clear impact of mineral fertiliser addition on bacterial co-occurrence structure. Most importantly, both organic amendments increased network complexity irrespective of mineral fertilisation regime. At the same time, the effects of manure and straw exhibited differences that might be explained by differences in their nutritional/chemical contents. It is concluded that bacterial interactions are a crucial parameter for the assessment of amendment effects regarding soil health and sustainability.

Bulk soil bacterial community mediated by plant community in Mediterranean ecosystem, Israel

The Israeli Mediterranean ecosystem has a distinctive flora with high levels of plant diversity. Previous studies of soil microbial ecology from the region have paid little attention to the possibility of distinctive soil bacterial communities associated with particular habitats. This study looked at bacterial communities present in the bulk soil from the closed canopy of four indigenous plants – Quercus ithaburensis, Calicotome villosa, Sarcopoterium spinosum, and Rhamnus puncata. Soil DNA was amplified for the 16S rRNA gene and sequenced using MiSeq Illumina platform. Results indicated that the bacterial communities differed between open and closed canopy with no significant difference in community structure within closed canopy, with soil moisture and organic matter content significantly influenced the community. Only the relative abundance of Gemmatimonadetes varied significantly with the open canopy having the highest abundance, and the relative abundance of Spartobacteria and Saprospirae was unusually high compared to other Mediterranean soils. There was no difference in OTU richness between plant species. Additionally, this study revealed that open canopy community between plants was nested within closed canopy bacterial community implying that open canopy community potentially serves as a source for the closed canopy. It is then possible that the rhizospheric influence extends beyond the root-soil interface and to the surrounding bulk soil. Overall, this study indicates that in Israeli Mediterranean ecosystems native plants extend a selection beyond the rhizosphere, and like other studies from Mediterranean ecosystems pH does not seem to play an integral role in structuring bacterial communities.

Crop Establishment Practices Are a Driver of the Plant Microbiota in Winter Oilseed Rape (Brassica napus).

Gaining a greater understanding of the plant microbiota and its interactions with its host plant heralds a new era of scientific discovery in agriculture. Different agricultural management practices influence soil microbial populations by changing a soil’s physical, chemical and biological properties. However, the impact of these practices on the microbiota associated with economically important crops such as oilseed rape, are still understudied. In this work we investigated the impact of two contrasting crop establishment practices, conventional (plow based) and conservation (strip–tillage) systems, on the microbiota inhabiting different plant microhabitats, namely rhizosphere, root and shoot, of winter oilseed rape under Irish agronomic conditions. Illumina 16S rRNA gene sequence profiling showed that the plant associated microhabitats (root and shoot), are dominated by members of the bacterial phyla Proteobacteria, Actinobacteria and Bacteroidetes. The root and shoot associated bacterial communities displayed markedly distinct profiles as a result of tillage practices. We observed a very limited ‘rhizosphere effect’ in the root zone of WOSR, i.e., there was little or no increase in bacterial community richness and abundance in the WOSR rhizosphere compared to the bulk soil. The two tillage systems investigated did not appear to lead to any major long term differences on the bulk soil or rhizosphere bacterial communities. Our data suggests that the WOSR root and shoot microbiota can be impacted by management practices and is an important mechanism that could allow us to understand how plants respond to different management practices and environments.