Species of Diaporthe (syn. Phomopsis) are important endophytes, saprobes and pathogens, infecting a wide range of plants and resulting in important crop diseases. However, the species occurring on pear remain largely unresolved. In this study, a total of 453 Diaporthe isolates were obtained from branches of Pyrus plants (including P. bretschneideri, P. communis, P. pyrifolia and P. ussuriensis collected from 12 provinces in China) showing shoot canker symptoms. Phylogenetic analyses based on five loci (ITS, TEF, CAL, HIS, and TUB) coupled with morphology of 113 representative isolates revealed that 19 Diaporthe species were isolated, representing 13 known species (including D. caryae, D. cercidis, D. citrichinensis, D. eres, D. fusicola, D. ganjae, D. hongkongensis, D. padina, D. pescicola, D. sojae, D. taoicola, D. unshiuensis and D. velutina) and six new species described here as D. acuta, D. chongqingensis, D. fulvicolor, D. parvae, D. spinosa and D. zaobaisu. Although Koch’s postulates confirmed all species to be pathogenic, a high degree of variation in aggressiveness was observed. Moreover, these species have a high diversity, plasticity, and prevalence related to the geographical location and pear species involved.

Host development influences gut microbial assemblies that may be confounded partly by dietary shifts and the changing environmental microbiota during ontogenesis. However, little is known about microbial colonization by excluding dietary effects and compositional differences in microbiota between the gut and environment at different ontogenetic stages. Herein, a developmental gut microbial experiment under controlled laboratory conditions was conducted with carnivorous southern catfish Silurus meridionalis fed on an identical prey with commensal and abundant microbiota. In this study, we provided a long-term analysis of gut microbiota associated with host age at 8, 18, 35, 65, and 125 day post-fertilization (dpf) and explored microbial relationships among host, food and water environment at 8, 35, and 125 dpf. The results showed that gut microbial diversity in southern catfish tended to increase linearly as host aged. Gut microbiota underwent significant temporal shifts despite similar microbial communities in food and rearing water during the host development and dramatically differed from the environmental microbiota. At the compositional abundance, Tenericutes and Fusobacteria were enriched in the gut and markedly varied with host age, whereas Spirochaetes and Bacteroidetes detected were persistently the most abundant phyla in food and water, respectively. In addition to alterations in individual microbial taxa, the individual differences in gut microbiota were at a lower level at the early stages than at the late stages and in which gut microbiota reached a stable status, suggesting the course of microbial successions. These results indicate that host development fundamentally shapes a key transition in microbial community structure, which is independent of dietary effects. In addition, the dominant taxa residing in the gut do not share their niche habitats with the abundant microbiota in the surrounding environment. It's inferred that complex gut microbiota could not be simple reflections of environmental microbiota. The knowledge enhances the understanding of gut microbial establishment in the developing fish and provides a useful resource for such studies of fish- or egg-associated microbiota in aquaculture.

Fish are the most widespread aquaculture species and maintain complex associations with microbial consortiums. However, the ecology of these associations present in multiple microhabitats in fish remains elusive, especially on the microbial assembly in fish external (skin and gill) and internal (stomach and intestine) niches, and the relationship with the rearing environment. To understand host dependence and niche differentiation of organ-specific microbiome signatures using a 16S rRNA gene-based sequencing technique, we systematically provided characterizations of a comparative framework relevant to the microbiome of stomach, regional intestine, skin, and gill in two important farmed fish species, herbivorous grass carp (Ctenopharyngodon idella) and carnivorous southern catfish (Silurus meridionalis), and of the rearing water. The different feeding habits of grass carp and southern catfish showed a significant separation of microbial community structure, with great compositional differences across body sites within each species. Site-driven divergences relied on host species: the same types of microhabitats between grass carp and southern catfish harbored differential microbiome. Additionally, body sites had remarkably distinct communities and displayed lower alpha diversity compared to rearing water. Unexpectedly, the stomach of southern catfish had the highest microbial diversity in the digestive tract of the two co-cultured fish species. For external sites within each species, a higher diversity occurred in gill of grass carp and in skin of southern catfish. Our results unveil different topographical microbiome signatures of the co-cultured species, indicating host selection in individual-level microbial assemblages and niche differentiation at the organ scale. This work represents a foundation for understanding the comprehensive microbial ecology of cohabiting farmed fish, suggesting potential applications associated with fish microbiome that urgently needs to be assessed in polycultured operations in aquaculture.

The fish intestinal microbiota is affected by dietary shifts or diet-related seasonal fluctuations making it highly variable and dynamic. It assists with the digestion and absorption of food that is a common, yet dynamic process. However, fundamental dynamics of microbial ecology associated with food digestion in intestine and stomach are poorly understood in fish. We selected the southern catfish, Silurus meridionalis, as the targeted species, owing to its foraging behavior with a large meal that can assure clear periodic rhythms in food digestion, to study spatial variations of the microbial community along the gastrointestinal (GI) tract. We further evaluated temporal microbial dynamics by collecting GI tract samples at time intervals 03, 12, and 24h after feeding. High-throughput sequencing results showed higher microbial diversity in the stomach than in the intestine and distinguishable community structures between stomach and intestine. Firmicutes were dominated by both Clostridium and unclassified Clostridiaceae, which was the most abundant taxon in the stomach, whereas Fusobacteria were dominated by Cetobacterium, which prevailed in the intestine. Firmicutes was significantly increased and Fusobacteria was decreased after feeding. Furthermore, inter-stomach microbial variability was greater than inter-intestine microbial variability. These results demonstrate that GI microbial assemblies are specific per anatomical site and are highly dynamic during food digestion, indicating that digestive status and/or sampling time are factors potentially influencing the microbial compositions. Furthermore, the finding of high spatial and temporal variations of the microbial community along the GI tract suggests limitations of single sampling regime to study food-derived microbial ecology.

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Pyrus bretschneideri cv. Dangshansuli is the most important commercial Asiatic pear cultivar worldwide. In recent years, a fruit rot disease of unknown etiology have caused considerable fresh market losses in the ‘Dangshansuli’ production operations in Dangshan county, Anhui Province, China. Fresh market losses typically range from 60 to 90% and in 2008 were estimated at US$150 million. Symptomatic mature ‘Dangshansuli’ pears were collected from an orchard in Dangshan County in February 2008. A thin section (about 1 mm3) of symptomatic tissue was sterilized in a bleach and placed on potato dextrose agar (PDA) medium for isolation. From all fruit, a single fungus was recovered displaying gray-white dense aerial mycelium. Identical fungi were isolated from six additional symptomatic ‘Dangshansuli’ pears collected from other orchards in the county. Pathogenicity tests using one isolate (DS-0) were conducted in triplicate by placing 4 mm diameter discs from 7-day-old PDA plates onto the mature ‘Dangshansuli’ pear fruit that were incubated in an incubator at 25°C with a 12-h photoperiod for 30 days. An equal number of noncolonized PDA inoculations were included as a control. Isolate DS-0 caused symptoms similar to those in the field within 7 days and complete collapse of cortical tissues within 30 days. No symptoms were observed on control fruit. Round brownish lesions with a diameter of about 3 cm on inoculated fruit was populated by sunken, rotiform acervuli on which numerous, colorless, oblong single cell shape conidia with width/length of 6 × 20 μm were produced. A comparison of morphology and sequence analysis of the ribosomal internal transcribed spacer (ITS) regions in pre- and post-inoculation cultures from inoculated fruit confirmed the presence DS-0. To further characterize DS-0, aliquots of extracted genomic DNA from the fungus were subjected to PCR amplification and sequencing of seven gene regions from the ITS, actin (ACT), β-tubulin 2 (TUB2), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), manganese-superoxide dismutase (SOD2), chitin synthase (CHS-1), and calmodulin (CAL), using the primers listed by Weir et al (4), except for the primer pair of ITS1 (5′-TCCGTAGGTGAACCTGCGG-3′) and ITS4 (5′-TCCTCCGCTTATTGATATGC-3′) for ITS amplification, and SODglo2-R (5′-TAGTACGCGTGCTCGGACAT-3′) and SODglo2-R (5′-TAGTACGCGTGCTCGGACAT-3′) for TBU2 amplification. Two or three clones of PCR products of each gene were sequenced and compared (GenBank Accession Nos. KC410780 to KC410786) to published data at http://www.cbs.knaw.nl/colletotrichum . The result indicated that DS-0 shared the highest similarity of 99.91% with Colletotrichum fructicola, corroborating numerous reports of Colletotrichum spp. causing bitter rot of pear on P. pyrifolia (1,2,3,4). C. fructicola was only recently reported as causing bitter rot of P. pyrifolia (4) and to our knowledge, this is the first report of C. fructicola causing bitter rot of P. bretschneideri, which will help producers select the best management practices for this devastating disease. References: (1) P. F. Cannon et al. Stud. Mycol. 73:181, 2012. (2) N. Tashiro et al. J. Gen. Plant Pathol. 78:221, 2012. (3) G. K. Wan et al. Mycobiology 35:238, 2007. (4) B. S. Weir et al. Stud. Mycol. 73:115, 2012.

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