Impacts of abiotic factors on the fungal communities of ‘Honeycrisp’ apples in Canada

The maintenance of the beneficial plant microbiome to control plant pathogens is an emerging concept of disease management, and necessitates a clear understanding of these microbial communities and the environmental factors that affect their diversity and compositional structure. As such, studies investigating the microbiome of economically significant cultivars within each growing region are necessary to develop adequate disease management strategies. Here, we assessed the relative impacts of growing season, management strategy, and geographical location on the fungal microbiome of ‘Honeycrisp’ apples from seven different orchard locations in the Atlantic Maritime Ecozone for two consecutive growing years. Though apple fruit tissue was dominated by relatively few fungal genera, significant changes in their fungal communities were observed as a result of environmental factors, including shifts in genera with plant-associated lifestyles (symbionts and pathogens), such as Aureobasidium, Alternaria, Penicillium, Diplodia, and Mycosphaerella. Variation in fungal composition between different tissues of fruit was also observed. We demonstrate that growing season is the most significant factor affecting fungal community structure and diversity of apple fruit, suggesting that future microbiome studies should take place for multiple growing seasons to better represent the host–microbiome of perennial crops under different environmental conditions.     

Global analysis of the apple fruit microbiome: are all apples the same?

We present the first worldwide study on the apple (Malus × domestica) fruit microbiome that examines questions regarding the composition and the assembly of microbial communities on and in apple fruit. Results revealed that the composition and structure of the fungal and bacterial communities associated with apple fruit vary and are highly dependent on geographical location. The study also confirmed that the spatial variation in the fungal and bacterial composition of different fruit tissues exists at a global level. Fungal diversity varied significantly in fruit harvested in different geographical locations and suggests a potential link between location and the type and rate of postharvest diseases that develop in each country. The global core microbiome of apple fruit was represented by several beneficial microbial taxa and accounted for a large fraction of the fruit microbial community. The study provides foundational information about the apple fruit microbiome that can be utilized for the development of novel approaches for the management of fruit quality and safety, as well as for reducing losses due to the establishment and proliferation of postharvest pathogens. It also lays the groundwork for studying the complex microbial interactions that occur on apple fruit surfaces.     

复合微生物菌剂对重茬苹果园土壤细菌群落的影响

【目的】了解抗重茬复合微生物菌剂对重茬苹果园土壤细菌数量及多样性的影响。【方法】对重茬苹果园土壤进行复合微生物菌剂处理后,采用自动核糖体内转录间隔区序列分析方法(Automated ribosomal intergenic spacer analysis,ARISA)对新茬苹果园、重茬苹果园土壤细菌群落多样性进行分析。【结果】经复合微生物菌剂处理2年后,重茬果园土壤OTUs总数和Shannon-Weiner指数分别为250和4.44,新茬果园OTUs总数和Shannon-Weiner指数分别为234和3.81,经One-Way ANOSIM法分析得到二者差异系数P分别为0.108 3和0.084 3。另外,重茬园和新茬园共享核心OTUs有89个,二者的Jaccard群落相似性系数为0.47,相似程度中等。【结论】复合微生物菌剂具有提高重茬果园土壤微生物多样性,促进重茬苹果园土壤微生物生态系统恢复的作用。     

Rootstock genotype succession influences apple replant disease and root-zone microbial community composition in an orchard soil

Apple replant disease (ARD) is a soil-borne disease complex that affects young apple trees in replanted orchards, resulting in stunted growth and reduced yields. Newly developed rootstock genotypes with tolerance to ARD may help to control this disease. We determined the effects of rootstock genotype rotations during orchard renovation, by investigating root-zone soil microbial consortia and the relative severity of ARD on seven rootstock genotypes (M.9, M.26, G.30, G.41, G.65, G.935, and CG.6210) planted in soil where trees on four of those same rootstocks (M.9, M.26, G.30 and CG.6210) had grown for the previous 15 years. Rootstock genotyping indicated that genetic distances among rootstocks were loosely correlated with their differential responses to ARD. Root-zone fungal and bacterial community composition, assessed by DNA fingerprinting (T-RFLP), differed between M.26 and CG.6210. Soil bacterial communities were influenced most by which rootstock had grown in the soil previously, while fungal communities were influenced more by the current replanted rootstock. In a clone library of bacteria from M.26 and CG.6210 root-zone soil, β-Proteobacteria was the most abundant phylum (25% of sequences). Sequences representing the Burkholderia cepacia complex were obtained only from CG.6210 soil. Rootstock genotypes that were grown in the orchard soil previously affected subsequent ARD severity, but replanting with the same or closely related rootstocks did not necessarily exacerbate this disease problem. Our results suggest that genotype-specific interactions with soil microbial consortia are linked with apple rootstock tolerance or susceptibility to ARD.     

Long-term orchard groundcover management systems affect soil microbial communities and apple replant disease severity

Apple replant disease (ARD) is a soil-disease syndrome of complex etiology that affects apple tree roots in replanted orchards, resulting in stunted tree growth and reduced yields. To investigate whether different groundcover management systems (GMSs) influence subsequent ARD severity, we grew apple seedlings in an outdoor nursery in pots containing orchard soil from field plots where four GMSs had been maintained for 14 years in an orchard near Ithaca, NY, USA. The GMS treatments were: (1) pre-emergence herbicide (Pre-H), bare soil strips maintained by applying tank-mixed glyphosate, norflurazon and diuron herbicides annually; (2) post-emergence herbicide (Post-H), sparse weed cover maintained by applying glyphosate in May and July each year; (3) mowed sod grass (Mowed Sod); and (4) bark mulch (Mulch). Soils were also sampled from the grass drive lane maintained between the trees in the orchard (Grass Lane). Sampled soils (Orchard soil) were either pasteurized or left untreated, placed into 4-L pots, and planted with one apple seedling per pot. After 3 months of growth, soil (Bioassay soil) and apple tree roots (Bioassay roots) were sampled from each pot and microbial populations colonizing samples were characterized. Seedling growth was reduced in soils sampled from all four GMS treatments compared to the Grass Lane soils. Among the GMS treatments, seedling biomass was greater in Pre-H than in the Post-H soil. Soil microbial communities and nutrient availability differed among all four GMS treatments and the Grass Lane. Root-lesion (Pratylenchus sp.) nematode populations were higher in the Mowed Sod than in the other GMS treatments. Soil bacterial and fungal community composition was assessed in Orchard and Bioassay soils and Bioassay roots with a DNA fingerprinting method (T-RFLP). Redundancy analysis indicated that soils sampled from the different GMS treatments differentially influenced seedling biomass. A clone library of 267 soil bacteria was developed from sampled Orchard soils and Bioassay roots. These communities were dominated by Acidobacteria (25% of sequences), Actinobacteria (19%), δ-Proteobacteria (12%), β-Proteobacteria (10%), and these ratios differed among the GMS soils. Members of the family Comamonadaceae were detected only in tree-row soil, not in the Grass Lanes. The dominant sequences among 145 cloned fungi associated with apple seedling roots were Fusarium oxysporum (16% of sequences), an uncultured soil fungus submitted under DQ420986 (12%), and Rhodotorula mucilaginosa (9%). In a redundancy analysis, factors including fungal and oomycete community compositions, soil respiration rates, population sizes of culturable bacteria and fungi, soil organic matter content, and nutrient availability, were not significant predictors of apple seedling biomass in these soils. Different GMS treatments used by apple growers may influence subsequent ARD severity in replanted trees, but edaphic factors commonly associated with soil fertility may not reliably predict tree-root health and successful establishment of replanted orchards.     

渭北塬区不同龄苹果园土壤微生物空间分布特征

以渭北塬区塬面5、10、15和20龄苹果园为对象,距树干1.0、1.5、2.0 m处用土钻法分层采集0—30 cm土样,稀释平板法测定土壤微生物数量,平行测定土壤有机碳、总氮和总磷,分析不同龄果园土壤微生物的空间分布状况及其与土壤碳、氮、磷的关系。结果表明:土壤真菌数量随树龄增大而增加,龄间差异显著(P0.05);与对照农田相比,各龄果园放线菌数量及5龄和20龄果园细菌数量偏低,10龄和15龄果园细菌数量偏高;各龄果园土壤真菌、细菌和放线菌数量均随深度增加而减小。就相同深度土层而言,真菌数量随果园年限增大而增加,细菌则以10龄和15龄果园较多,同深度土层的放线菌龄间差异随深度增加而减小。在沿树干向外的径向水平方向上,真菌数量随果园年限的增加相应增多;10龄和15龄果园土壤细菌和放线菌高于5龄果园和20龄果园。5龄果园土壤总氮有沿树干向外、沿表层向下逐步降低的趋势,果园从5龄经10龄到15龄,其"高氮点"则逐步向外、向下移动。塬区果园土壤C∶N比偏低。     

Secondary metabolites and nutrients explain fungal community composition in aspen wood

Fungi are the main decomposers of litter and wood, driving carbon and nutrient cycles. Despite a large number of studies, fungal community composition is remarkably difficult to predict. In the present study, we explore the importance of secondary metabolites and nutrient content in wood and bark as determinants of fungal community composition. We used aspen (Populus tremula) logs of similar size, from one location, and measured concentrations of carbon, nitrogen and secondary metabolites in bark and wood sampled shortly after felling. Fungal DNA was extracted from logs directly after felling and after two seasons of decomposition, and the fungal communities were assessed using DNA-metabarcoding. Concentrations of metabolites varied considerably between individual trees, and we also observed significant differences within single trees. Plant metabolites and nitrogen concentrations significantly affected fungal community composition. For the overall fungal communities and for wood saprotrophic fungi, the explanatory power of wood and bark metabolites was highest in logs decomposed over two seasons. In recently felled trees however, concentration of metabolites had a stronger effect on plant pathogens and endophytes. We conclude that secondary metabolites represent an overlooked, but important niche dimension for fungal communities in both functional sapwood and dead wood.     

Palmitic acid mediated change of rhizosphere and alleviation of Fusarium wilt disease in watermelon

Palmitic acid (PA) in root exudates or decaying residues can reduce the incidence of soil-borne diseases and promote the growth of some crop plants. However, the effects of PA on soil-borne pathogens and microbial communities are poorly understood. Here, we investigate the effects of PA on overall watermelon microbial communities and the populations of Fusarium oxysporum f.sp. niveum (Fon). The effects of PA on the mycelial growth and spore production of Fon were tested in vitro, while its effects on Fon, total bacteria and total fungi populations, and microbial communities were evaluated in a pot experiment. The results revealed that all test concentrations of PA inhibited Fon mycelia growth and spore production. The pot experiment showed that 0.5 mM and 1 mM PA reduced Fon but increased total bacteria populations, and 0.5 mM and 1 mM PA 0.5 mM and 1 mM PA promoted the change to a soil type of bacteria soil. Meanwhile, 0.5 mM PA and 1 mM PA altered the community composition of the rhizosphere microorganisms and reduced the relative abundance of two bacterial operational taxonomic units (OTUs) and the two fungal OTUs that were significantly (p < 0.01) related with disease severity and increased that of four bacterial OTUs and the two fungal that were highly significantly (p < 0.01) negatively correlated with the disease severity. These results suggest that application of PA decreased the populations of Fon, changed the rhizosphere microbial composition, reduced the disease severity of Fusarium wilt, and promoted the growth of watermelon.     

Resilience of the Natural Phyllosphere Microbiota of the Grapevine to Chemical and Biological Pesticides

The phyllosphere is colonized by complex microbial communities, which are adapted to the harsh habitat. Although the role and ecology of nonpathogenic microorganisms of the phyllosphere are only partially understood, leaf microbiota could have a beneficial role in plant growth and health. Pesticides and biocontrol agents are frequently applied to grapevines, but the impact on nontarget microorganisms of the phyllosphere has been marginally considered. In this study, we investigated the effect of a chemical fungicide (penconazole) and a biological control agent (Lysobacter capsici AZ78) on the leaf microbiota of the grapevine at three locations. Amplicons of the 16S rRNA gene and of the internal transcribed spacer were sequenced for bacterial and fungal identification, respectively. Pyrosequencing analysis revealed that the richness and diversity of bacterial and fungal populations were only minimally affected by the chemical and biological treatments tested, and they mainly differed according to grapevine locations. Indigenous microbial communities of the phyllosphere are adapted to environmental and biotic factors in the areas where the grapevines are grown, and they are resilient to the treatments tested. The biocontrol properties of phyllosphere communities against downy mildew differed among grapevine locations and were not affected by treatments, suggesting that biocontrol communities could be improved with agronomic practices to enrich beneficial populations in vineyards.     

Agrichemical impact on growth and survival of non-target apple phyllosphere microorganisms

The impact of conventional agrichemicals commonly used in New Zealand apple production on non-target, culturable phyllosphere microbial populations was studied in the laboratory (agar, leaf, and seedling assays) and field (apple orchard). Morphologically distinct bacteria (three), yeasts (five), and filamentous microfungi (two) were used as indicator species. The agar assay showed that agrichemical toxicity to microorganisms was dependent on product type, product rate, and organism studied. While the fungicides metiram and captan stopped or severely reduced growth of nearly all microorganisms studied, the insecticides tebufenozide and lufenuron and the fungicide nitrothal-isopropyl showed the least amount of microbial toxicity, each affecting 2 of the 10 indicator organisms studied. In the leaf assay a single agrichemical application at field rate either reduced or increased microbial population counts, again depending on product and microorganism. Repeated agrichemical applications, however, reduced microbial population numbers from 10- to 10,000-fold in planta. Further field research validated these findings, although differences in microbial numbers before and after agrichemical applications were less dramatic. In the orchard, total organism numbers recovered within 2-6 days, but species richness (sum of recognizable taxonomic units) declined. Agrichemicals clearly affected non-target, culturable surface microorganisms. The importance of diversity and stability of microbial populations for disease control still needs to be established.     

Streptomycin Application Has No Detectable Effect on Bacterial Community Structure in Apple Orchard Soil

Streptomycin is commonly used to control fire blight disease on apple trees. Although the practice has incited controversy, little is known about its nontarget effects in the environment. We investigated the impact of aerial application of streptomycin on nontarget bacterial communities in soil beneath streptomycin-treated and untreated trees in a commercial apple orchard. Soil samples were collected in two consecutive years at 4 or 10 days before spraying streptomycin and 8 or 9 days after the final spray. Three sources of microbial DNA were profiled using tag-pyrosequencing of 16S rRNA genes: uncultured bacteria from the soil (culture independent) and bacteria cultured on unamended or streptomycin-amended (15 μg/ml) media. Multivariate tests for differences in community structure, Shannon diversity, and Pielou''s evenness test results showed no evidence of community response to streptomycin. The results indicate that use of streptomycin for disease management has minimal, if any, immediate effect on apple orchard soil bacterial communities. This study contributes to the profile of an agroecosystem in which antibiotic use for disease prevention appears to have minimal consequences for nontarget bacteria.     

不同品种苹果树内生细菌群落多样性及功能

【背景】目前苹果树内生细菌的研究较多,但对不同品种苹果树内生细菌群落多样性分析比较的相关报道还较少。【目的】通过分析比较新疆本地和吉尔吉斯斯坦引进的8个不同品种苹果树内生细菌群落多样性的差异,可以充分挖掘其蕴含的丰富微生物资源。【方法】采用MiSeq高通量测序技术分别测定不同品种苹果树内生细菌群落16S rRNA基因V3-V4区序列并进行生物信息学分析。【结果】不同品种苹果树中获得的V3-V4区有效序列数在61487-71583条之间,聚成24-92个操作分类单元(operationaltaxonomicunit,OTU),Shannon指数和Simpson指数分别在0.729-1.177和0.265-0.457之间,新疆本地品种的苹果树内生细菌种类和多样性高于吉尔吉斯斯坦品种。内生细菌种群分析结果表明,变形菌门和放线菌门的OTU总计分别覆盖了不同品种苹果树内生细菌的61.16%-97.08%,为苹果树的主要优势细菌门。优势细菌属数目、组成及其丰度随苹果品种的不同而有所差异。马赛菌属(Massilia)和节杆菌属(Arthrobacter)的总丰度最高,其丰度分别在6.06%-71.37%、1.29%-17.86%之间,且优势细菌属中存在具有一定促生抗逆或与降解环境有毒有害物质相关的有益功能性状的微生物类群。群落功能预测分析初步显示不同品种的苹果树内生细菌群落功能有所差异,新疆本地品种微生物群落的功能信息多于吉尔吉斯斯坦品种,主要体现在化能异养、需氧化能异养、尿素分解、砷酸盐解毒和异化砷还原等功能方面。此外,这8个品种苹果树内生菌中可能还存在大量的未知属,其范围在13.74%-69.60%之间。【结论】不同品种苹果树内生细菌群落多样性较为丰富,种群组成和功能存在较大差异,且潜在分类信息也给新的微生物资源挖掘和功能分析提供线索,值得进一步研究。     

Linking Soil Biotic and Abiotic Factors to Apple Replant Disease: a Greenhouse Approach

Apple replant disease (ARD) is a frequently occurring plant disease, which causes retarded growth and mortality of young apple trees in replanted orchards. The aetiology is not well understood, but soil‐borne micro‐organisms are often discussed as primary causal agents of the replant problem. A greenhouse study was conducted in Laimburg, Italy, with orchard soils from the region, with the aim of obtaining information about the influence of soil biotic and abiotic factors on the aetiology of the disease. Apple rootstocks (M9) were planted into soils cultivated with apple trees that were either fumigated with chloropicrin or not fumigated, as well as mixtures of fumigated and non‐fumigated soils. In addition, uncultivated soils (from the inter‐row, from a fallow plot and from a meadow) were taken as controls. Various parameters were measured after 62 days in a controlled pot assay. Soils fumigated with chloropicrin resulted in higher apple shoot growth and lower microbial biomass carbon than non‐fumigated soils. Uncultivated soils had generally the highest microbial biomass carbon and the highest ergosterol contents. No considerable differences between basal respiration, ergosterol content, pH, electrical conductivity, and most nutrient and metal contents were observed between fumigated and non‐fumigated soils. Denaturing gradient gel electrophoresis gels of DNA extracted from the soils revealed differences in the fungal, bacterial and actinobacterial communities of the different soils, indicating significant shifts in microbial community composition after chloropicrin treatment. This study indicates biotic factors in soil to be a causal agent of apple replant disease.     

Soil and bark biodiversity forms discrete islands between vineyards that are not affected by distance or management regime

Within geographic regions, the existing data suggest that physical habitat (bark, soil, etc.) is the strongest factor determining agroecosystem microbial community assemblage, followed by geographic location (site), and then management regime (organic, conventional, etc.). The data also suggest community similarities decay with increasing geographic distance. However, integrated hypotheses for these observations have not been developed. We formalized and tested such hypotheses by sequencing 3.8 million bacterial 16S, fungal ITS2 and non-fungal eukaryotic COI barcodes deriving from 108 samples across two habitats (soil and bark) from six vineyards sites under conventional or conservation management. We found both habitat and site significantly affected community assemblage, with habitat the stronger for bacteria only, but there was no effect of management. There was no evidence for community similarity distance–decay within sites within each habitat. While communities significantly differed between vineyard sites, there was no evidence for between site community similarity distance–decay apart from bark bacterial communities, and no correlations with soil and bark pH apart from soil bacterial communities. Thus, within habitats, vineyard sites represent discrete biodiversity islands, and while bacterial, fungal and non-fungal eukaryotic biodiversity mostly differs between sites, the distance by which they are separated does not define how different they are.     

Culturing captures members of the soil rare biosphere

The ecological significance of rare microorganisms within microbial communities remains an important, unanswered question. Microorganisms of extremely low abundance (the 'rare biosphere') are believed to be largely inaccessible and unknown. To understand the structure of complex environmental microbial communities, including the representation of rare and prevalent community members, we coupled traditional cultivation with pyrosequencing. We compared cultured and uncultured bacterial members of the same agricultural soil, including eight locations within one apple orchard and four time points. Our analysis revealed that soil bacteria captured by culturing were in very low abundance or absent in the culture-independent community, demonstrating unexpected accessibility of the rare biosphere by culturing.     

Significant and persistent impact of timber harvesting on soil microbial communities in Northern coniferous forests

Forest ecosystems have integral roles in climate stability, biodiversity and economic development. Soil stewardship is essential for sustainable forest management. Organic matter (OM) removal and soil compaction are key disturbances associated with forest harvesting, but their impacts on forest ecosystems are not well understood. Because microbiological processes regulate soil ecology and biogeochemistry, microbial community structure might serve as indicator of forest ecosystem status, revealing changes in nutrient and energy flow patterns before they have irreversible effects on long-term soil productivity. We applied massively parallel pyrosequencing of over 4.6 million ribosomal marker sequences to assess the impact of OM removal and soil compaction on bacterial and fungal communities in a field experiment replicated at six forest sites in British Columbia, Canada. More than a decade after harvesting, diversity and structure of soil bacterial and fungal communities remained significantly altered by harvesting disturbances, with individual taxonomic groups responding differentially to varied levels of the disturbances. Plant symbionts, like ectomycorrhizal fungi, and saprobic taxa, such as ascomycetes and actinomycetes, were among the most sensitive to harvesting disturbances. Given their significant ecological roles in forest development, the fate of these taxa might be critical for sustainability of forest ecosystems. Although abundant bacterial populations were ubiquitous, abundant fungal populations often revealed a patchy distribution, consistent with their higher sensitivity to the examined soil disturbances. These results establish a comprehensive inventory of bacterial and fungal community composition in northern coniferous forests and demonstrate the long-term response of their structure to key disturbances associated with forest harvesting.     

Orchard floor management practices that maintain vegetative or biomass groundcover stimulate soil microbial activity and alter soil microbial community composition

Groundcover management systems (GMS) are important in managing fruit-tree orchards because of their effects on soil conditions, nutrient availability, tree growth and yields. We employed a polyphasic approach, incorporating measures of soil microbial abundance, activity and community composition, to study the long-term effects of different GMS on biotic and abiotic factors in an orchard soil. Four GMS treatments – Pre-emergence residual herbicides (Pre-H), post-emergence herbicide (Post-H), mowed-sod (Grass), and hardwood bark mulch (Mulch) – were established in 2-m-wide strips within tree rows in an apple orchard in 1992, and have been maintained and monitored annually until the present. We have measured soil water and nutrient availability, tree growth, and yields annually from 1993 to 2003. Soil nematode numbers and trophic groups were evaluated in July and Oct. 2001, and Sept. 2003. Numbers of culturable bacteria and fungi, soil respiratory activity, eubacterial and fungal community composition were determined in May and Sept. 2003. The Pre-H treatment soil had the fewest culturable bacteria, while the Grass treatment had the largest population of culturable fungi. Soil nematode population size and diversity were also affected by GMS treatments; the Pre-H treatment had the lowest ratio of (bacteriovores + fungivores) to plant parasitic nematodes. Soil respiration rates were higher in the Mulch than in other treatments during a 40-day incubation period. Hierarchical cluster dendrograms of denaturing gradient gel electrophoresis (DGGE) fingerprints for eubacterial community 16S rRNA genes indicated that Post-H and Grass treatments clustered together and separately from the Pre-H and Mulch treatments, which were also grouped together. The influence of GMSs on the fungal community, as assessed by PCR-DGGE of the internal transcribed spacer (ITS) region, was not as pronounced as that observed for bacteria. Soil fungal community composition under the Mulch differed from that under other treatments. The effects of GMS on soil microbial community abundance, activity, and composition were associated with observed differences in soil organic matter inputs and turnover, nutrient availability, and apple tree growth and yields under the different GMS treatments.     

Changes in populations of soil microorganisms,nematodes, and enzyme activity associated with application of powdered pine bark

Evaluation of enzyme activities in combination with taxonomic analyses may help define the mechanisms involved in microbial decomposition of orgaic amendments and biological control of soilborne pathogens. In this study, powdered pine bark was added to nematode-infested soil at rates of 0, 5, 10, 15, 20, 25, 30, 35, 40, 45, and 50 g kg^–1. Total fungal populations did not differ among treatments immediately after application of pine bark. After 7 days, fungal populations were positively correlated with increasing levels of pine bark. This increase was sustained through 14 and 21 days.Penicillium chrysogenum andPaecilomves variotii were the predominant fungal species isolated from soil amended with pine bark. Total bacterial populations did not change with addition of pine bark at 0, 7, and 14 days after treatment. At 21 and 63 days, total bacterial populations declined in soil receiving the highest rates of pine bark. Addition of pine bark powder to soil caused a shift in predominant bacterial genera fromBacillus spp. in nonamended soil, toPseudomonas spp. in amended soil. Soil enzyme activities were positively correlated with pine bark rate at all sampling times. Trehalase activity was positively correlated with total fungal populations and with predominant fungal species, but was not related to bacterial populations. The number of non-parasitic (non-stylet bearing) nematodes andMeloidogyne arenaria in soil and roots were not correlated with pine bark rate. However,Heterodera glycines juveniles in roots, and the number of cysts g^–1 root, declined with increasing levels of pine bark.Journal Series Series No. 18-933598 Alabama Agricultural Experiment Station     

Positive correlation between soil bacterial metabolic and plant species diversity and bacterial and fungal diversity in a vegetation succession on Karst

The hypothesis that positive links exist among plant taxonomic diversity, belowground microbial taxonomic and metabolic diversities was tested for four secondary vegetation successional stages (tussock (T), shrub (S), secondary forest (SF) and primary forest (PF)) in Huanjiang county, SW China. Soil bacterial communities were characterized by DNA fingerprinting and metabolic profiling. Along the succession, Shannon diversity indices followed the order SF>PF>S>T for plant taxonomic diversity, T>SF>PF>S for bacterial operational taxonomic diversity, SF>T>S>PF for fungal operational taxonomic diversity, and SF>PF>S>T for bacterial metabolic diversity. Significant positive correlations were found between bacterial and fungal taxonomic diversities. However, there was no significant correlation between soil microbial taxonomic diversity and bacterial metabolic diversity. Two-way ANOVA revealed that vegetation and season, as well as their interaction, had significant effects on soil microbial (fungal and bacterial) taxonomic diversities, but that there were no seasonal effects on metabolic diversity. However, PCA and MANOVA revealed highly significant differences among the bacterial community-level physiological profiles, reflecting the successional sequence. The findings from this survey support the notion that there are strong interactions between aboveground and belowground communities and suggest that bacterial metabolic and plant taxonomic diversities, but not microbial taxonomic and metabolic diversities, can be correlated.     

Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe,China)

1. Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood.
2. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large-scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish-farming lake in mid-eastern China.
3. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind-mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities.
4. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally-driven environmental variables including water temperature and nutrient availability.