Endophytic Bacterial Diversity in Rice (Oryza sativa L.) Roots Estimated by 16S rDNA Sequence Analysis

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

印度块菌-云南松菌根际土壤细菌的种群组成和群落结构

以印度块菌-云南松菌根际土壤细菌为研究对象,研究其种群组成和结构特征。(1)稀释平板法分离得到印度块菌-云南松菌根际土壤细菌的纯培养菌株,对菌株的16S rRNA序列测序分析,对测序的菌株数量和得到的OTUs数量绘制物种累积曲线,当物种累积曲线趋于平缓时,对OTUs进行系统发育分析,揭示可培养细菌的种群组成和结构特征。(2)对印度块菌-云南松菌根际土壤细菌16S rRNA基因的V3—V4区进行高通量测序,分析全部细菌类群的种群组成和结构特征。(1)分离得到菌根际可培养细菌793株,分属于3个属的61个OTUs,其中假单胞菌属(Pseudomonas)序列占总序列的86%,不动杆菌属(Acinetobacter)序列占总序列的9.8%,链霉菌属(Streptomyces)序列占总序列的6.5%。假单胞菌是印度块菌-云南松菌根际土壤可培养细菌的绝对优势类群。(2)高通量测序得到菌根际细菌序列8937条,分属于20个门、198属、2073个OTUs。隶属于变形菌门(Proteobacteria)、放线菌门(Actinobacteria)和酸杆菌门(Acidobacteria)的OTUs占总OTUs的65.9%,变形菌门、放线菌门和酸杆菌门细菌是印度块菌-云南松菌根际土壤细菌的优势细菌。隶属于黄杆菌属(Flavobacterium)、根瘤菌属(Rhizobium)和假黄色单胞菌属(Pseudoxanthomona)的OTUs占总OTUs的33%,黄杆菌属、根瘤菌属和假黄色单胞菌属细菌是印度块菌-云南松菌根际土壤细菌的优势属。印度块菌-云南松菌根际土壤可培养细菌多样性较低,假单胞菌属细菌占据绝对优势地位。印度块菌-云南松菌根际土壤细菌类群具有较高的多样性,物种种类丰富,优势菌群集中。     

Phylogenetic Diversity of Bacteria Associated with the Marine Sponge <Emphasis Type="Italic">Gelliodes carnosa</Emphasis> Collected from the Hainan Island Coastal Waters of the South China Sea

Several molecular techniques were employed to document the bacterial diversity associated with the marine sponge Gelliodes carnosa. Cultivation-dependent and cultivation-independent methods were used to obtain the 16S rRNA gene sequences of the bacteria. Phylogenetic analysis based on the 16S rRNA gene sequences showed that the bacterial community structure was highly diverse with representatives of the high G + C Gram-positive bacteria, cyanobacteria, low G + C Gram-positive bacteria, and proteobacteria (α-, β-, and γ-), most of which were also found in other marine environments, including in association with other sponges. Overall, 300 bacterial isolates were cultivated, and a total of 62 operational taxonomic units (OTUs) were identified from these isolates by restriction fragment length polymorphism (RFLP) analysis and DNA sequencing of the 16S rRNA genes. Approximately 1,000 16S rRNA gene clones were obtained by the cultivation-independent method. A total of 310 clones were randomly selected for RFLP analysis, from which 33 OTUs were acquired by further DNA sequencing and chimera checking. A total of 12 cultured OTUs (19.4% of the total cultured OTUs) and 13 uncultured OTUs (39.4% of the total uncultured OTUs) had low sequence identity (≤97%) with their closest matches in GenBank and were probably new species. Our data provide strong evidence for the presence of a diverse variety of unidentified bacteria in the marine sponge G. carnosa. A relatively high proportion of the isolates exhibited antimicrobial activity, and the deferred antagonism assay showed that over half of the active isolates exhibited a much stronger bioactivity when grown on medium containing seawater. In addition to demonstrating that the sponge-associated bacteria could be a rich source of new biologically active natural products, the results may have ecological implications. This study expands our knowledge of the diversity of sponge-associated bacteria and contributes to the growing database of the bacterial communities within sponges.     

不同水稻组织内生细菌的群落多样性

[目的]为详细了解水稻不同组织内生细菌群落多样性。[方法]对宁粳43号内生细菌的总DNA提取后,采用高通量测序技术对水稻内生细菌的16S rRNA基因进行了序列测定,分析了水稻不同组织部位内生细菌群落结构特征。[结果]叶部共获得内生细菌OTUs 610个,茎部411个,根部174个。物种分类显示,叶部内生细菌种类隶属于22门40纲103目198科399属,其中优势类群是红球菌属（Rhodococcus）和乳酸杆菌属（Lactobacillus）,它们的相对丰度分别为21.00%和9.19%;茎部内生细菌种类隶属于19门31纲85目169科306属,其中优势类群是红球菌属和罗尔斯通菌属（Ralstonia）,它们的相对丰度分别为19.25%和13.52%;根部内生细菌种类隶属于9门19纲44目82科140属,其中优势类群是肠杆菌属（Enterobacter）和埃希氏杆菌属（Escherichia）,它们的相对丰度分别为81.13%和10.89%。根茎叶中相同的OTU有78个,放线菌门（Actinobacteria）与大多数细菌具有相关性。根系内生细菌中具有调控各种代谢网络功能的物种丰度高于茎部和叶部。[结论]不同水稻组织内生细菌具有丰富的群落多样性,其中叶部的内生细菌物种最丰富,根系参与各种代谢调控的细菌丰度最高,各个组织部位的优势菌属各不相同,变形菌门是最重要的水稻内生细菌。     

基于高通量测序分析西藏沙棘根瘤内生菌的多样性

根瘤是微生物侵染植物根部并与之形成的共生结构,这些微生物都可被称为植物内生菌。豆科植物根瘤中的内生菌常常又被称为根瘤菌,而侵染非豆科植物形成根瘤的主要是放线菌弗兰克氏菌,这些非豆科植物又被称为放线菌结瘤植物。西藏沙棘是一种典型的放线菌结瘤植物,由于其分布生境的特殊性,对其根瘤内生菌的研究具有重要的生态意义。对于西藏沙棘根瘤内生菌的研究,培养方法因难以模拟自然条件而不易获得纯培养,高通量测序技术对其多样性的研究提供了便利。因此,本研究以生长在甘肃省天祝县金强河河滩地的西藏沙棘根瘤为材料,采用16S rRNA基因扩增子高通量测序方法,结合OTU分析,对西藏沙棘根瘤内生菌的多样性进行探讨。实验结果表明,西藏沙棘根瘤内生菌具有丰富的多样性,根瘤内的优势属为共生固氮的弗兰克氏菌属（Frankia）,其相对丰度为47.63%,共检测到7个弗兰克氏菌属的OTUs;根瘤内除弗兰克氏菌外,还存在大量的非弗兰克氏菌,共检测到1523个OTUs,隶属于22个门、33个纲、69个目、113个科和202个属,相对丰度排名前9的属中有25个非弗兰克氏菌属的OTUs。该研究也表明,西藏沙棘根瘤内生菌具有丰富的多样性,西藏沙棘根瘤中不仅存在着可共生固氮的弗兰克氏菌,并且还分布着非弗兰克氏菌;在同一根瘤样品中,弗兰克氏菌属还具有不同的物种。本研究不仅拓展了西藏沙棘根瘤内生菌多样性的研究方法,还为同一寄主植物中弗兰克氏菌多样性的研究提供了分析思路。     

Evidence for a conserved microbiota across the different developmental stages of Plodia interpunctella

Diversity and composition of lepidopteran microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the microbiota among different developmental stages of the Indian meal moth, Plodia interpunctella, which is considered one of the major pest of commodities world-wide. Using culture-independent approach based on Illumina 16S rRNA gene sequencing we characterized the microbiota of four developmental stages: eggs, first-, and last-instar larvae, and adult. A total of 1022 bacterial OTUs were obtained, showing a quite diversified microbiota associated to all the analyzed stages. The microbiotas associated with P. interpunctella resulted almost constant throughout the developmental stages, with approximately 77% of bacterial OTUs belonging to the phylum of Proteobacteria. The dominant bacterial genus is represented by Burkholderia (?64%), followed by Propionibacterium, Delftia, Pseudomonas, and Stenotrophomonas. A core bacterial community, composed of 139 OTUs, was detected in all the developmental stages, among which 112 OTUs were assigned to the genus Burkholderia. A phylogenetic reconstruction, based on the 16S rRNA, revealed that our Burkholderia OTUs clustered with Burkholderia cepacia complex, in the same group of those isolated from the hemipterans Gossyparia spuria and Acanthococcus aceris. The functional profiling, predicted on the base of the bacterial 16S rRNA, indicates differences in the metabolic pathways related to metabolism of amino acids between preimaginal and adult stages. We can hypothesize that bacteria may support the insect host during preimaginal stages.     

Biocontrol Potential of Soybean Bacterial Endophytes Against Charcoal Rot Fungus, <Emphasis Type="Italic">Rhizoctonia bataticola</Emphasis>

A total of 137 bacterial isolates from surface sterilized root, stem, and nodule tissues of soybean were screened for their antifungal activity against major phytopathogens like Rhizoctonia bataticola, Macrophomina phaseolina, Fusarium udam, and Sclerotium rolfsii. Nine bacterial endophytes suppressed the pathogens under in vitro plate assay. These were characterized biochemically and identified at the genus level based on their partial sequence analysis of 16S rDNA. Eight of the isolates belonged to Bacillus and one to Paenibacillus. The phylogenetic relationship among the selected isolates was studied and phylogenetic trees were generated. The selected isolates were screened for biocontrol traits like production of hydrogen cyanide (HCN), siderophore, hydrolytic enzymes, antibiotics, and plant growth promoting traits like indole 3-acetic acid production, phosphate solubilization, and nitrogen fixation. A modified assessment scheme was used to select the most efficient biocontrol isolates Paenibacillus sp. HKA-15 (HKA-15) and Bacillus sp. HKA-121 (HKA-121) as potential candidates for charcoal rot biocontrol as well as soybean plant growth promotion.     

Differential bacterial endophytome in Foc-resistant banana cultivar displays enhanced antagonistic activity against Fusarium oxysporum f.sp. cubense (Foc)

Diverse endophytes with multiple functions exist in different banana cultivars. However, the diversity of cultivable bacterial endophytome that contributes to antifungal activity against Fusarium oxysporum f.sp. cubense (Foc) in resistant and susceptible banana cultivars is mostly unknown. In the present study, we isolated bacterial endophytes from resistant Yengambi KM5 (AAA) and susceptible banana cultivar Ney Poovan (AB) to determine the diversity of cultivable bacterial endophytes. Our study revealed the presence of 56 cultivable bacterial endophytes and 6 nectar-associated bacteria in YKM5 and 31 cultivable bacterial endophytes in Ney Poovan. The identified cultivable bacterial genera in YKM5 included Alcaligenes, Arthrobacter, Azotobacter, Acinetobacter, Agrobacterium, Bacillus, Brucella, Brevundimonas, Brachybacterium, Beijerinckia, Klebsiella, Leclercia, Lysinibacillus, Myroides, Ochrobactrum, Pseudomonas, Rhizobium, Stenotrophomonas, Serratia, and Verticiella. In Ney Poovan, the cultivable endophytic bacterial genera present were Agrobacterium, Bacillus, Bradyrhizobium, Enterobacter, Klebsiella, Lysinibacillus, Micrococcus, Ochrobactrum, Pseudomonas, Rhizobium, and Sphingobium. Thus, the composition and diversity of cultivable endophytic bacterial genera were higher in Foc-resistant YKM5. The antifungal efficacy of bacterial endophytes Brachybacterium paraconglomeratum YEBPT2 (65.5%), Brucella melitensis YEBPS3 (63.3%), Bacillus velezensis YEBBR6 (63.3%), and nectar-associated Bacillus albus YEBN2 (61.1%) from YKM5 showed the highest antifungal activity against Foc, compared with the antifungal activity of endophytes from the susceptible cultivar.     

The Endophytic Mycoflora of Bark,Leaf, and Stem Tissues of <Emphasis Type="Italic">Azadirachta indica</Emphasis> A. Juss (Neem) from Varanasi (India)

A systematic study was made of the endophytes of Azadirachta indica A. Juss (the neem tree) growing in several of its natural habitats in India. A total of 233 isolates of endophytic fungi representing 18 fungal taxa were obtained from segments of bark, stem, and leaves of this tree. Hyphomycetes (62.2%) were the most prevalent followed by the Coelomycetes (27.4%) and Mycelia Sterilia (7.7%). As mathematically determined, the maximum species richness and frequency of colonization of endophytes appeared in leaf segments rather than stem and bark tissues from each location. Endophytic colonization frequency was also greater in leaves (45.5%) than bark (31.5%). The leaf samples from all locations were nearly constant in their endophytic composition, whereas bark samples showed maximum diversity at different locations. Inter-site comparisons for endophytic diversity, however, were not significantly different with Loc1 and Loc2 having a maximum of 66.67% J _c. The smallest similarity was between Loc2 and Loc3 of 54.17% J _c. The dominant endophytic fungi isolated were Phomopsis oblonga, Cladosporium cladosporioides, Pestalotiopsis sp., Trichoderma sp, and Aspergillus sp. Genera such as Periconia, Stenella, and Drechslera are reported here for the first time as endophytes from this host plant. This report illustrates the value of sampling different tissues of a given plant in several locations to obtain the greatest species diversity of endophytes. The rich and sizeable collection of endophytic fungi from this specific plant may represent a unique source of one or more of the interesting and useful bioactive compounds normally associated with A. indica such as the azadirachtins and related tetranortriterpenoids.     

Di Alcuni Caratteri Differenziali Nelle Plantule di “ Cuscuta Epithymum „ Mürr. e di “ Cuscuta Pentagona „ Eng.

Endophytes are micro-organisms that colonize the internal tissues of plants without inducing signs of negative effects and that can provide benefits to plant health and yield. In the present work, the culturable bacterial endophyte community, colonizing vegetative organs of grapevine, was isolated from surface-sterilized plant tissues and characterized by molecular methods. From roots, shoots and leaves of Vitis vinifera “Glera”, located in six different vineyards throughout the Conegliano-Valdobbiadene DOCG area (Veneto, Italy), 381 culturable strains were successfully isolated; amplified ribosomal DNA restriction analysis and nucleotide sequencing showed that approximately 30% of the endophyte community belonged to the genus Bacillus, which was the most represented; other genera such as Staphylococcus, Microbacterium, Paenibacillus, Curtobacterium, Stenotrophomonas, Variovorax, Micrococcus and Agrococcus were identified. Endophyte community composition within each vine was different in respect to other endophyte populations living in grapevine plants coming from different vineyards; moreover, the bacterial composition changed depending on the season of sampling. The above data highlight the great diversity of culturable bacterial species inhabiting Glera grapevines and open the way for a characterization and selection of strains that could potentially be used to improve the vineyard management for plant growth and yield, plant responses to stresses, biocontrol and biofertilization.     

Metamicrobiomics in herbivore beetles of the genus Cryptocephalus (Chrysomelidae): toward the understanding of ecological determinants in insect symbiosis

The Cryptocephalus marginellus (Coleoptera: Chrysomelidae) complex is composed by six species that are supposed to have originated by events of allo‐ or parapatric speciation. In the present study we investigated the alternative hypotheses that the bacterial communities associated with six populations of this species complex are shaped by environmental factors, or reflect the proposed pattern of speciation. The microbiota associated with the six populations, from five species of the complex, have been characterized through 16S rRNA pyrotag sequencing. Based on a 97% sequence similarity threshold, data were clustered into 381 OTUs, which were analyzed using a variety of diversity indices. The microbiota of C. acquitanus and C. marginellus (Calanques) were the most diverse (over 100 OTUs), while that from C. zoiai yielded less bacterial diversity (45 OTUs). Taxonomic assignment revealed Proteobacteria, Tenericutes and Firmicutes as the dominant components of these beetles’ microbiota. The most abundant genera were Ralstonia, Sphingomonas, Rickettsia, and Pseudomonas. Different strains of Rickettsia were detected in C. eridani and C. renatae. The analysis of β‐diversity revealed high OTU turnover among the populations of C. marginellus complex, with only few shared species. Hierarchical clustering taking into account relative abundances of OTUs does not match the phylogeny of the beetles, therefore we hypothesize that factors other than phylogenetic constraints play a role in shaping the insects’ microbiota. Environmental factors that could potentially affect the composition of bacterial communities were tested by fitting them on the results of a multi‐dimensional scaling analysis. No significant correlations were observed towards the geographic distances or the host plants, while the composition of the microbiota appeared associated with altitude. The metabolic profiles of the microbiotas associated with each population were inferred from bacterial taxonomy, and interestingly, the obtained clustering pattern was consistent with the host phylogeny.     

Shared and unique features of bacterial communities in native forest and vineyard phyllosphere

Phyllosphere bacteria have received little attention despite their important roles in shaping plant performance traits. In this study, we characterize the bacterial communities on leaves of native trees inhabiting sclerophyllous forests in central Chile, one of the world's biodiversity hotspots. Additionally, we provide profiles of bacterial communities on grape leaves and berries of organic and conventional vineyards. Results of 16S rRNA gene amplicon sequence analysis showed that 45% of OTUs were shared across forest leaves, grape leaves, and grape berries. Conventional management had higher number of OTUs shared with forest leaves than organic management. In addition, grape leaves subjected to conventional management had higher alpha diversity than those with organic management, while no significant effect of agricultural management was observed in grape berries. Indicator analysis showed that Bdellovibrio, Beijerinckia, and Spirosoma were typical for forest leaves, whereas Enhydrobacter, Delftia, Proteiniclasticum, Arsenicicoccus, and Alkaliphilus were typical for the vineyard phyllosphere. Regarding agricultural managements, Beijerinckia, Sedimentibacter, Nesterenkonia, Gluconobacter, Conexibacter, and Anaeromyxobacter were typical for conventional grape leaves, whereas no genus‐level indicator was found for organic vineyard leaves. These results provide new insights of the diversity patterns of the phyllosphere microbiome in native and cultivated lands and suggest that both of these microbiomes are connected and integrated systems.     

Comparison of the diversity,composition, and host recurrence of xylariaceous endophytes in subtropical,cool temperate,and subboreal regions in Japan

The diversity, composition, and host recurrence of endophytic fungi in the Xylariaceae were compared in subtropical (ST), cool temperate (CT), and subboreal forests (SB) in Japan based on the 28S ribosomal DNA sequences from fungal isolates. A total of 610 isolates were obtained from the leaves of 167 tree species in three sites, which were classified into 42 operational taxonomic units (OTUs) at the 99 % similarity level of the 28S rDNA sequence. ST, CT, and SB yielded 31, 13, and three OTUs, respectively. The OTU richness, diversity, and evenness of fungal communities were in the order: ST > CT > SB. The 42 OTUs were assigned to nine genera in the Xylariaceae: Xylaria, Annulohypoxylon, Anthostomella, Biscogniauxia, Nemania, Hypoxylon, Muscodor, Daldinia, and Rosellinia. Xylarioid isolates in the subfamily Xylarioideae outnumbered Hypoxyloid isolates in the subfamily Hypoxyloideae in ST and CT, whereas the opposite was found in SB. Sørensen’s quotient of similarity was generally low between the three sites. Host recurrence of fungal OTUs was evaluated with the degree of specialization of interaction network between xylariaceous endophytes and plant species and compared between the three sites. We found that the networks in the three sites showed a significantly higher degree of specialization than simulated networks, where partners were associated randomly. Permutational multivariate analyses of variance indicated that plant family and leaf trait significantly affected the OTU composition in ST, which can account for the specialization of interaction network and host recurrence of xylariaceous endophytes.     

Surveying the Microbiome of Ants: Comparing 454 Pyrosequencing with Traditional Methods To Uncover Bacterial Diversity

We are only beginning to understand the depth and breadth of microbial associations across the eukaryotic tree of life. Reliably assessing bacterial diversity is a key challenge, and next-generation sequencing approaches are facilitating this endeavor. In this study, we used 16S rRNA amplicon pyrosequencing to survey microbial diversity in ants. We compared 454 libraries with Sanger-sequenced clone libraries as well as cultivation of live bacteria. Pyrosequencing yielded 95,656 bacterial 16S rRNA reads from 19 samples derived from four colonies of one ant species. The most dominant bacterial orders in the microbiome of the turtle ant Cephalotes varians were Rhizobiales, Burkholderiales, Opitutales, Xanthomonadales, and Campylobacterales, as revealed through both 454 sequencing and cloning. Even after stringent quality filtering, pyrosequencing recovered 445 microbe operational taxonomic units (OTUs) not detected with traditional techniques. In comparing bacterial communities associated with specific tissues, we found that gut tissues had significantly higher diversity than nongut tissues, and many of the OTUs identified from these groups clustered within ant-specific lineages, indicating a deep coevolutionary history of Cephalotes ants and their associated microbes. These lineages likely function as nutritional symbionts. One of four ant colonies investigated was infected with a Spiroplasma sp. (order Entomoplasmatales), a potential ant pathogen. Our work shows that the microbiome associated with Cephalotes varians is dominated by a few dozen bacterial lineages and that 454 sequencing is a cost-efficient tool to screen ant symbiont diversity.     

Isolation,molecular characterization and virome analysis of culturable wood fungal endophytes in esca symptomatic and asymptomatic grapevine plants

Europe is the world largest grape producer, but in recent years, the report of diseases due to infection by grapevine trunk pathogens (GTPs) is becoming one of the main constraints for viticulture. Among grapevine trunk diseases (GTDs), esca syndrome is one of the most complex, characterized by simultaneous infection of several fungi, which leads to important reduction in yield and quality. Previous characterization of fungal isolates associated with esca syndrome leads to the recognition of at least three important players: Phaeocremonium minimum, Phaemoniella chlamydospora and Fomitiporia mediterranea. Here we isolated and characterized molecularly fungal endophytes directly from field wood tissues of plants showing or not esca symptoms. In addition, to better characterize such collection, a deep RNA sequencing (100 M reads in paired-end) to screen for mycovirus presence was performed. Thirty-nine viral genomes were detected, 38 of which were putative new viral species; some of these viruses infected GTPs, including P. minimum and F. mediterranea. In this work, we reported for the first time a curated collection of grapevine fungal endophytes identifying the associated mycoviruses some of which could be employed in future biotechnological exploitation as biological control agents for sustainable plant protection.     

A meta-analysis of the microbial diversity observed in anaerobic digesters

In this study, the collective microbial diversity in anaerobic digesters was examined using a meta-analysis approach. All 16S rRNA gene sequences recovered from anaerobic digesters available in public databases were retrieved and subjected to phylogenetic and statistical analyses. As of May 2010, 16,519 bacterial and 2869 archaeal sequences were found in GenBank. The bacterial sequences were assigned to 5926 operational taxonomic units (OTUs, based on ?97% sequence identity) representing 28 known bacterial phyla, with Proteobacteria (1590 OTUs), Firmicutes (1352 OTUs), Bacteroidetes (705 OTUs), and Chloroflexi (693 OTUs) being predominant. Archaeal sequences were assigned to 296 OTUs, primarily Methanosaeta and the uncharacterized WSA2 group. Nearly 60% of all sequences could not be classified to any established genus. Rarefaction analysis indicates that approximately 60% of bacterial and 90% of archaeal diversity in anaerobic digesters has been sampled. This analysis of the global bacterial and archaeal diversity in AD systems can guide future studies to further examine the microbial diversity involved in AD and development of comprehensive analytical tools.     

Comparison of bacterioplankton communities in three mariculture ponds farming different commercial animals in subtropical Chinese coast

In order to explore the responses of the bacterioplankton community to different types of aquaculture environments, three mariculture ponds comprised of groupers (Epinephelus diacanthus, ED), prawns (Penaeus vannamei, PV), and abalone (Haliotis diversicolor supertexta, HDS) in southeast, coastal China were investigated. The free-living bacterial diversity was analyzed through the construction of 16S rDNA clone library. A total of 203 16S rDNA sequences from three clone libraries were classified into 118 operational taxonomic units (OTUs), of which 51, 31, and 42 OTUs were distributed in the ED, PV, and HDS pond, respectively, with Bacteroidetes (30.6%), Actinobacteria (55.2%), and Cyanobacteria (32.8%) as the dominant division in the respective ponds. Meanwhile, each pond occupied some unique OTUs that were affiliated with uncommon (sub-)phyla, such as candidate OP11 division, Acidobacteria, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia. Bacterial diversity in the ED pond was the richest, followed by the HDS and the PV pond. OTUs of 61.9% and 94.9% have less than 90% and 97% similarity to their nearest neighbors in public databases, respectively. All OTUs were grouped into 67 clusters, covering 11 (sub-)phyla. The OTUs only from single pond distributed in 53 clusters (79.1%), the OTUs shared by two ponds were affiliated with 14 clusters (20.9%), and none of clusters was formed by the OTUs which commonly originated from the three pond libraries, suggesting that the composition of bacterial populations in these ponds were significantly different. These results indicate that the aquatic environment created by different mariculture animals may foster very special and complex bacterial communities. Handling editor: David Philip Hamilton     

Molecular assessment of microbiota structure and dynamics along mixed olive oil and winery wastewaters biotreatment

The major parcel of the degradation occurring along wastewater biotreatments is performed either by the native microbiota or by added microbial inocula. The main aim of this study was to apply two fingerprinting methods, temperature gradient gel electrophoresis (TGGE) and length heterogeneity-PCR (LH-PCR) analysis of 16S rRNA gene fragments, in order to assess the microbiota structure and dynamics during mixed olive oil and winery wastewaters aerobic biotreatment performed in a jet-loop reactor (JLR). Sequence homology analysis showed the presence of bacterial genera Gluconacetobacter, Klebsiella, Lactobacillus, Novosphingobium, Pseudomonas, Prevotella, Ralstonia, Sphingobium and Sphingomonas affiliated with five main phylogenetic groups: alpha-, beta- and gamma-Proteobacteria, Firmicutes and Bacteroidetes. LH-PCR analysis distinguished eight predominant DNA fragments correlated with the samples showing highest performance (COD removal rates of 67 up to 75%). Cluster analysis of both TGGE and LH-PCR fingerprinting profiles established five main clusters, with similarity coefficients higher than 79% (TGGE) and 62% (LH-PCR), and related with hydraulic retention time, indicating that this was the main factor responsible for the shifts in the microbiota structure. Canonical correspondence analysis revealed that changes observed on temperature and O₂ level were also responsible for shifts in microbiota composition. Community level metabolic profile analysis was used to test metabolic activities in samples. Integrated data revealed that the microbiota structure corresponds to bacterial groups with high degradative potential and good suitability for this type of effluents biotreatments.     

Conventional farming impairs Rhizoctonia solani disease suppression by disrupting soil food web

Intensive farming in agriculture raises questions in relation to environmental sustainability and the widespread use of agrochemicals. In the present work, we compare the impact of organic and intensive farming, in connection to the soil suppressiveness against the soilborne pathogen Rhizoctonia solani. Three farms were considered in the study: two practicing organic cultivation (for 10 and 20 years, respectively), and one applying conventional cultivation. Soil suppressiveness was assessed in a greenhouse bioassay with lettuce (Lactuca sativa). Soil microbiome was characterized by combining BIOLOG EcoPlates^? with high‐throughput sequencing of bacterial and eukaryotic rRNA gene markers. Suppressiveness towards R. solani was higher in organic than in conventional farming soil, but this property was lost after soil sterilization. Functional biodiversity was significantly higher in the two organic soils, and this parameter was predictive of the suppressiveness towards R. solani. According to our analyses, the overall microbial taxonomic diversity was unlinked to suppressiveness. A correlation analysis, carried out at the genus level for the most abundant bacterial and eukaryotic microbial taxa, showed that 58.7% of the genera had a statistically significant correlation with suppressiveness. In particular, the genera Flavisolibacter, Massilia, Pseudomonas, Ramlibacter, Rhizophus and the oligochaete worms belonging to the Enchytraeidae family positively correlated with the disease suppression.