Caught in the tides: the (re)development of a trepang (sea cucumber, <Emphasis Type="Italic">Holothuria scabra</Emphasis>) industry at Warruwi,Northern Territory

From at least the late 1700s, Indigenous people from the West Arnhem region of the Northern Territory (Australia) engaged with Macassan trepang (sea cucumber, Holothuria scabra) traders, who visited the coastline each wet season. A Methodist Mission was established at Warruwi, in West Arnhem Land, in 1916. The Mission actively participated in the collection and sale of trepang, and the industry continued through the twentieth century in a changed form. Over recent decades the trade has been dominated by an interstate commercial operator with no Indigenous involvement. This paper outlines past and present engagements in the trepang industry by the Indigenous residents of the remote community of Warruwi. It discusses contemporary efforts to develop a community-based small-scale trepang fishery and the challenges faced in doing so. Trepang is seen as linking people’s past to their futures, and the development of a trepang enterprise is seen as a way to draw on important sea country and kin based relationships whilst contributing to a secure and sustainable future. A number of gains have been made towards these ends. But as in previous eras, the nature of the industry reflects its contemporary context and the opportunities and challenges this presents. Capacity and legal issues present obstacles characteristic of the difficulties Indigenous Australian communities face in leveraging the resources necessary to undertake local development initiatives.     

Composition and Stability of the Microbial Community inside the Digestive Tract of the Aquatic Crustacean <Emphasis Type="Italic">Daphnia magna</Emphasis>

Small filter-feeding zooplankton organisms like the cladoceran Daphnia spp. are key members of freshwater food webs. Although several interactions between Daphnia and bacteria have been investigated, the importance of the microbial communities inside Daphnia guts has been studied only poorly so far. In the present study, we characterised the bacterial community composition inside the digestive tract of a laboratory-reared clonal culture of Daphnia magna using 16S rRNA gene libraries and terminal-restriction length polymorphism fingerprint analyses. In addition, the diversity and stability of the intestinal microbial community were investigated over time, with different food sources as well as under starvation stress and death, and were compared to the community in the cultivation water. The diversity of the Daphnia gut microbiota was low. The bacterial community consisted mainly of Betaproteobacteria (e.g. Limnohabitans sp.), few Gammaproteobacteria (e.g. Pseudomonas sp.) and Bacteroidetes that were related to facultatively anaerobic bacteria, but did not contain typical fermentative or obligately anaerobic gut bacteria. Rather, the microbiota was constantly dominated by Limnohabitans sp. which belongs to the Lhab-A1 tribe (previously called R-BT065 cluster) that is abundant in various freshwaters. Other bacterial groups varied distinctly even under constant cultivation conditions. Overall, the intestinal microbial community did not reflect the community in the surrounding cultivation water and clustered separately when analysed via the Additive Main Effects and Multiplicative Interaction model. In addition, the microbiota proved to be stable also when Daphnia were exposed to bacteria associated with a different food alga. After starvation, the community in the digestive tract was reduced to stable members. After death of the host animals, the community composition in the gut changed distinctly, and formerly undetected bacteria were activated. Our results suggest that the Daphnia microbiota consists mainly of an aerobic resident bacterial community which is indigenous to this habitat.     

The Intestinal Bacterial Community in the Food Waste-Reducing Larvae of <Emphasis Type="Italic">Hermetia illucens</Emphasis>

As it is known that food waste can be reduced by the larvae of Hermetia illucens (Black soldier fly, BSF), the scientific and commercial value of BSF larvae has increased recently. We hypothesised that the ability of catabolic degradation by BSF larvae might be due to intestinal microorganisms. Herein, we analysed the bacterial communities in the gut of BSF larvae by pyrosequencing of extracting intestinal metagenomic DNA from larvae that had been fed three different diets. The 16S rRNA sequencing results produced 9737, 9723 and 5985 PCR products from larval samples fed food waste, cooked rice and calf forage, respectively. A BLAST search using the EzTaxon program showed that the bacterial community in the gut of larvae fed three different diets was mainly composed of the four phyla with dissimilar proportions. Although the composition of the bacterial communities depended on the different nutrient sources, the identified bacterial strains in the gut of BSF larvae represented unique bacterial species that were unlike the intestinal microflora of other insects. Thus, our study analysed the structure of the bacterial communities in the gut of BSF larvae after three different feedings and assessed the application of particular bacteria for the efficient degradation of organic compounds.     

Fisheries and reserves of the Far Eastern sea cucumberApostichopus japonicus

An analysis of fishery reports and the observations of scuba divers permanently employed in fishing for the Far Eastern sea cucumber (trepang) shows that fishing forA. japonicus in Amurskii and Pos'et bays over the last seven years has resulted in catches of 122 to 373 t/year. The price for trepang has steadily risen over these seven years, from $2 US in 1992 to $5 in 1999; the money turnover in the area of criminal trepang fishing has ranged between $244000 to $1492000. The fraction of trepang obtained in southern Primorye constitutes about 0.35% of the global catch of holothurians.     

Distribution Pattern of Far Eastern Sea Cucumber Apostichopus japonicus in Busse Lagoon (Southern Sakhalin)

We analyzed the distribution pattern and size structure in aggregations of the far eastern sea cucumber (trepang), Apostichopus japonicus in Busse Lagoon (Southern Sakhalin). Trepang populations, which differ in their size composition and population density, have been grouped by their spatial differentiation. It has been shown that in the absence of solid substrates in the lagoon, the animals gather on substrates such as the alga Ahnfeltia tobuchiensis and on clusters of the oyster Crassostrea gigas. It is found that on the southeastern part of the lagoon, trepang makes up an extensive aggregation confined to the bed of Ahnfeltia; the distribution of the holothurians mostly has a random pattern. In the northwestern part of the lagoon, trepang makes up aggregations on oyster and algal beds; the distribution of these aggregations shows a random pattern.     

Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection

The gut microbiotas of zebrafish and mice share six bacterial divisions, although the specific bacteria within these divisions differ. To test how factors specific to host gut habitat shape microbial community structure, we performed reciprocal transplantations of these microbiotas into germ-free zebrafish and mouse recipients. The results reveal that communities are assembled in predictable ways. The transplanted community resembles its community of origin in terms of the lineages present, but the relative abundance of the lineages changes to resemble the normal gut microbial community composition of the recipient host. Thus, differences in community structure between zebrafish and mice arise in part from distinct selective pressures imposed within the gut habitat of each host. Nonetheless, vertebrate responses to microbial colonization of the gut are ancient: Functional genomic studies disclosed shared host responses to their compositionally distinct microbial communities and distinct microbial species that elicit conserved responses.     

土壤细菌网络互作调控线虫肠道细菌群落

动物肠道细菌群落在联系宿主与生态系统功能中发挥着至关重要的作用。【目的】本研究旨在评估绿肥翻压和水稻生长不同时期对土壤细菌和线虫肠道细菌群落组成和结构的影响,并探究土壤细菌和线虫肠道细菌群落间的潜在关联关系。【方法】基于盆栽试验,结合16S rRNA基因高通量测序技术,分析黑麦草翻压和对照处理下水稻生长的前期(返青期)和后期(收获期)土壤细菌和线虫肠道细菌群落,结合网络分析研究土壤细菌网络互作对线虫肠道细菌群落的潜在影响。【结果】黑麦草翻压对土壤细菌和线虫肠道细菌群落组成和结构没有显著影响(P>0.05);水稻生长后期样品比前期样品具有更高的α多样性。基于随机森林机器学习法获得的土壤细菌和线虫肠道细菌生物标志物之间存在广泛的显著相关关系,为土壤细菌群落变化调控线虫肠道细菌群落组成提供了有力的证据。共现网络分析表明土壤细菌之间的正相互作用显著促进了土壤细菌和线虫肠道细菌之间的正相互作用(P<0.01),进而影响了线虫肠道细菌之间的网络互作。结构方程模型进一步表明土壤养分含量的降低主要通过降低土壤细菌之间正相互作用,从而间接影响线虫肠道细菌之间的互作。【结论】土壤细菌互作可能在...     

Autochthonous bacterial flora indicated by PCR-DGGE of 16S rRNA gene fragments from the alimentary tract of Costelytra zealandica (Coleoptera: Scarabaeidae)

Aims: To locate and identify putative autochthonous bacteria within the grass grub gut that may have a role in symbiosis. Methods and Results: Polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) fingerprinting was used to investigate bacterial diversity in the grass grub larval gut. The microbial community profiles from five geographically distinct populations were compared and the influence of feeding was analysed. Bacterial community in the midgut was highly variable between locations and was affected by feeding. The hindgut contained a more diverse but stable bacterial community that was less affected by external conditions. Forty-seven distinct DGGE bands, representing different bacterial genotypes, could be distinguished from all samples, with 34 different bands occurring in the hindgut. The 22 most common bands were isolated and DNA was sequenced. Sequence analysis revealed that most bacteria (16/22) were affiliated to the Clostridiales with the predominant bacteria affiliated to the genus Clostridium. The remaining bacteria were aligned to the Betaproteobacteria, Deltaproteobacteria and Bacteroidetes. Conclusions: The grass grub larva has an autochthonous microflora with predominance of Clostridium spp. in the hindgut. Significance and Impact of the Study: Occurrence of an autocthonous microflora in the grass grub hindgut suggests a symbiotic relationship which could help explain the ability of larval scarabs to feed on recalcitrant organic matter.     

Effects of anthropogenic habitat disturbance and Giardia duodenalis infection on a sentinel species' gut bacteria

Habitat disturbance, a common consequence of anthropogenic land use practices, creates human–animal interfaces where humans, wildlife, and domestic species can interact. These altered habitats can influence host–microbe dynamics, leading to potential downstream effects on host physiology and health. Here, we explored the effect of ecological overlap with humans and domestic species and infection with the protozoan parasite Giardia duodenalis on the bacteria of black and gold howler monkeys (Alouatta caraya), a key sentinel species, in northeastern Argentina. Fecal samples were screened for Giardia duodenalis infection using a nested PCR reaction, and the gut bacterial community was characterized using 16S rRNA gene amplicon sequencing. Habitat type was correlated with variation in A. caraya gut bacterial community composition but did not affect gut bacterial diversity. Giardia presence did not have a universal effect on A. caraya gut bacteria across habitats, perhaps due to the high infection prevalence across all habitats. However, some bacterial taxa were found to vary with Giardia infection. While A. caraya's behavioral plasticity and dietary flexibility allow them to exploit a range of habitat conditions, habitats are generally becoming more anthropogenically disturbed and, thus, less hospitable. Alterations in gut bacterial community dynamics are one possible indicator of negative health outcomes for A. caraya in these environments, since changes in host–microbe relationships due to stressors from habitat disturbance may lead to negative repercussions for host health. These dynamics are likely relevant for understanding organism responses to environmental change in other mammals.     

非人灵长类肠道菌群组成及影响因素

与其他哺乳动物一样,非人灵长类肠道内含有复杂的细菌群落,与其营养和健康密切相关。非人灵长类肠道菌群研究具有生态和保护的双重意义。近十几年来,得益于分子生物学研究方法的成熟和应用,非人灵长类肠道菌群研究发展迅速。本文总结了非人灵长类肠道菌群组成及其四个主要影响因素的最新研究成果。研究表明,非人灵长类肠道菌群基本上是由来自12个门的细菌组成的,其中,拟杆菌门(Bacteroidetes)、厚壁菌门(Firmicutes)和变形菌门(Proteobacteria)是优势菌门。这些菌门包括数目繁杂的下级阶元,总体上,不同非人灵长类的肠道菌群组成在科和属水平上的相似度比在门水平上低得多。有些菌科和菌属在某些非人灵长类的肠道菌群中所占比例特别高,这些细菌往往与宿主的食物消化紧密相关。非人灵长类肠道菌群组成受到宿主种类及其系统发育关系、食性、年龄与性别、社会互动等因素的重要影响。最后,针对相关研究现状,本文提出了有待于深入探讨的研究问题。我国非人灵长类肠道菌群研究相对滞后,希望本文对推进国内相关研究有所贡献。     

Bacterial flora of newly caught Antarctic fish Notothenia neglecta

Summary The heterotrophic bacterial flora of Antarctic fish Notothenia neglecta was studied in Potter Cove (King George Island, South Shetland Islands). Quantitative and qualitative analysis of aerobic bacteria from sea water, skin, stomach and intestine were carried out. In addition, anaerobic flora of stomach and intestine was studied and compared. Pseudomonas was dominant in sea water samples but, neither skin nor digestive tract samples showed to be rich in this genus. Stomach flora showed variable results between samples. The gut flora was composed almost exclusively of Vibrio. Despite extreme environmental conditions this Antarctic fish show an intestinal indigenous microflora very similar to warmer waters fish. Several factors, that we discussed, could be determining the Vibrio dominance in the gut of marine teleosts.     

Characterization of Bacteria That Suppress Rhizoctonia Damping-Off in Bark Compost Media by Analysis of Fatty Acid Biomarkers

Examination of cucumber roots (Cucumis sativus L.) grown in bark compost media and of the surrounding edaphic substrate showed profiles of polar lipid fatty acids commonly found in bacteria. The composition of fatty acids in these profiles differed significantly between roots grown in a medium naturally suppressive to Rhizoctonia damping-off and roots from a conducive medium. Cucumber roots from the suppressive medium had higher proportions of cis-vaccenic acid (18:1 ω 7c) and the iso-branched monoenoic fatty acid i17:1 ω 8 but lower proportions of several iso- and anteiso-branched fatty acids compared with roots from the conducive medium. The concentrations of the bacterial fatty acids were significantly lower in the surrounding media. However, the suppressive and conducive growth substrates had differences in the composition of the bacterial fatty acids similar to those found between the cucumber roots proper. These results suggest major differences in bacterial community composition between suppressive and conducive systems. Fatty acid analyses were also utilized to examine the effects on bacterial community composition of root colonization by Flavobacterium balustinum 299, a biocontrol agent. The concentration of the most prominent fatty acid in this bacterium, i17:1 ω 8, was increased on roots produced from inoculated seeds in a medium rendered suppressive by the treatment. This change was concomitant with a significant increase in the concentration of 18:1 ω 7c, not present in the lipids of the antagonist, indicating a shift in the microflora from a conducive to a suppressive bacterial community.     

The Gut Bacterial Community of Mammals from Marine and Terrestrial Habitats

After birth, mammals acquire a community of bacteria in their gastro-intestinal tract, which harvests energy and provides nutrients for the host. Comparative studies of numerous terrestrial mammal hosts have identified host phylogeny, diet and gut morphology as primary drivers of the gut bacterial community composition. To date, marine mammals have been excluded from these comparative studies, yet they represent distinct examples of evolutionary history, diet and lifestyle traits. To provide an updated understanding of the gut bacterial community of mammals, we compared bacterial 16S rRNA gene sequence data generated from faecal material of 151 marine and terrestrial mammal hosts. This included 42 hosts from a marine habitat. When compared to terrestrial mammals, marine mammals clustered separately and displayed a significantly greater average relative abundance of the phylum Fusobacteria. The marine carnivores (Antarctic and Arctic seals) and the marine herbivore (dugong) possessed significantly richer gut bacterial community than terrestrial carnivores and terrestrial herbivores, respectively. This suggests that evolutionary history and dietary items specific to the marine environment may have resulted in a gut bacterial community distinct to that identified in terrestrial mammals. Finally we hypothesize that reduced marine trophic webs, whereby marine carnivores (and herbivores) feed directly on lower trophic levels, may expose this group to high levels of secondary metabolites and influence gut microbial community richness.     

Diversity and temporal stability of bacterial communities in a model passerine bird, the zebra finch

The composition and dynamics of the gastrointestinal bacterial communities in birds is determined by both host-specific and environmental exposure factors yet these are poorly understood. We selected the zebra finch, Taeniopygia guttata, as the host species to examine the diversity and temporal stability of the faecal microflora in a bird, owing to its importance as a model organism in avian ecology, neuroscience and evolution studies. The stability of the gut bacterial community of individual male and female zebra finches was assessed through repeat faecal sampling via culture and temperature gradient gel electrophoresis and partial sequencing of PCR-amplified eubacterial 16S rRNA gene products. Nineteen bacterial genera were detected across all samples (n = 99), with each bird carrying on average six operational taxonomic units. Using a novel statistical approach, we showed that bacterial assemblages and community richness varied between individual birds but remained stable over time within individuals. Neither the composition nor richness of bacterial communities differed significantly between the sexes. Our results show that zebra finches housed together under controlled conditions show consistent variation between individuals in their gut microflora that is not attributable to differences in host exposure to environmental microbial sources. Future studies could usefully explore the origin of this individual-specific variation and its consequences for host fitness and sexual selection.     

人工饲养恒河猴幼猴不同肠段微生物宏基因组学研究

目的以恒河猴幼猴为模型,采用16S rRNA宏基因组方法探讨十二指肠、盲肠、直肠的菌群组成。方法收集4例健康幼猴十二指肠、盲肠、直肠样本,提取细菌总DNA,采用新一代高通量测序技术对16S rRNA基因的V3-V4高变区测序,分析比较菌群结构及多样性。结果 (1)门水平各肠段微生物优势菌群主要为硬壁菌门、变形菌门及拟杆菌门,在各肠段中的占比总和超过88%;(2)属水平,十二指肠中以芽胞杆菌属等为优势菌属,盲肠中以螺杆菌属、颤杆菌属、孢杆菌属等为优势菌属,直肠中以乳酸菌属、链球菌属、颤杆菌属等为优势菌属;(3)各肠段微生物功能差异较大,十二指肠主要承担营养物质的消化吸收,盲肠主要承担细胞及遗传物质的合成,直肠主要承担调节机体免疫力、抗感染等功能。结论各肠段菌群组成差异较大;各肠段细菌功能差异较大,且与其生理功能有一定关联;在肠道菌群研究中,应充分考虑粪便样品微生物的组成是否能够完全代表肠道微生物的组成。     

Cold stress-induced changes in the aerobic heterotrophic gastrointestinal tract bacterial flora of red hybrid tilapia

Fifteen juvenile red hybrid tilapia Oreochromis mossambicus × O. macrochir averaging 50 g body weight were cold-stressed by immersion in 18° C sea water; control fish ( n = 15) were kept at the acclimation temperature of 26° C. Three fish from each group were killed 0, 24, 48 and 72 h after the start of the experiment. Gastrointestinal tracts were removed and dissected into the stomach, anterior gut and posterior gut regions. Aerobic heterotrophic bacteria were identified and enumerated relative to temperature, exposure time and gastrointestinal tract region. Gram negative genera included Alcaligenes, Flavobacterium, Photobacterium, Pseudomonas and Vibrio ; the latter three were predominant. Mean bacterial numbers and taxonomic composition of the microflora varied significantly ( P <0·05) in response to the three test variables. There were greater mean total bacterial numbers at 18 than at 26° C, due primarily to proliferation of Vibrio spp. Mean bacterial numbers after 24 h were greater than those at both the earlier and later sampling periods. Mean bacterial numbers in the stomach were less than those in the anterior and posterior gut, which were not significantly different. The relative abundance of Vibrio spp. was negatively correlated with that of Flavobacterium , which may have reflected competition between pathogenic and nonpathogenic species. Such stress-induced changes in the bacterial microflora may contribute to the onset of disease because several species of Vibrio are known primary or opportunistic fish pathogens.     

The inconstant gut microbiota of Drosophila species revealed by 16S rRNA gene analysis

The gut microorganisms in some animals are reported to include a core microbiota of consistently associated bacteria that is ecologically distinctive and may have coevolved with the host. The core microbiota is promoted by positive interactions among bacteria, favoring shared persistence; its retention over evolutionary timescales is evident as congruence between host phylogeny and bacterial community composition. This study applied multiple analyses to investigate variation in the composition of gut microbiota in drosophilid flies. First, the prevalence of five previously described gut bacteria (Acetobacter and Lactobacillus species) in individual flies of 21 strains (10 Drosophila species) were determined. Most bacteria were not present in all individuals of most strains, and bacterial species pairs co-occurred in individual flies less frequently than predicted by chance, contrary to expectations of a core microbiota. A complementary pyrosequencing analysis of 16S rRNA gene amplicons from the gut microbiota of 11 Drosophila species identified 209 bacterial operational taxonomic units (OTUs), with near-saturating sampling of sequences, but none of the OTUs was common to all host species. Furthermore, in both of two independent sets of Drosophila species, the gut bacterial community composition was not congruent with host phylogeny. The final analysis identified no common OTUs across three wild and four laboratory samples of D. melanogaster. Our results yielded no consistent evidence for a core microbiota in Drosophila. We conclude that the taxonomic composition of gut microbiota varies widely within and among Drosophila populations and species. This is reminiscent of the patterns of bacterial composition in guts of some other animals, including humans.     

Bacteria present in the gut of two neotropicalCephalotini ants,Cephalotes atratus andZacryptocerus cf.pusillus

Insects have varied patterns of gut design and some of them allow the establishment of a fermentative microflora. Anaerobically cultured digestive bacteria fromCephalotes atratus andZacryptocerus cf.pusillus were counted, isolated and characterized. Individuals from both species had a density of 10⁵ bacteria per gram of digestive organ (ventriculum, ileum and rectum). Bacterial strains were mostly facultative anaerobes and H₂S producers, and had no cellulolytic nor uric acid degrading activities. Primary mixed cultures from the gut ofC. atratus had wider tolerance to pH and temperature variations than Z. cf.pusillus, which was consistent with characteristics regarding its digestive microbial composition and its habitat.     

舟山群岛不同功能区划海域细菌群落结构分析

浮游细菌在海洋生态系统中不可或缺,在海洋生物地球化学循环过程中起着关键性作用。【目的】为了解舟山群岛不同功能区划海域细菌群落结构及丰度变化,探索海洋生态因子对细菌群落结构的影响。【方法】于2016年夏季(8月)在舟山群岛不同功能区划海域共设置8个典型站位采集表层海水,基于细菌16S rRNA基因进行高通量测序;利用流式细胞术揭示各海域细菌丰度;利用典范对应分析(Canonical correspondence analysis,CCA)探讨海洋生态因子与细菌多样性之间的关系。【结果】共获取到305487条原始序列,基于97%相似性水平进行OTU(Operational Taxonomic Units)聚类分析,共得到1088个OTUs,包括29个门、62个纲、138个目、239个科、416个属。细菌群落组成在各个站位之间不尽相同,但都主要包括Flavobacteria、Alphaproteobacteria、Gammaproteobacteria三大优势菌纲。CCA结果表明细菌群落结构和多样性情况与站位分布和所在站位的环境因子息息相关,Cyanobacteria受硝酸盐影响显著,Parcubacteria受温度影响最大,而磷酸盐对本实验海域菌群影响甚微。对海洋菌群潜在功能进行预测的结果显示,各海域菌群在氨基酸代谢、碳水化合物代谢、膜运输等方面功能较为突出,为今后舟山海洋微生物研究提供了新的方向。【结论】高通量测序分析可以更精确地揭示海洋菌群的群落结构信息。该研究为细菌群落结构与环境因素的关联提供参考。本研究所取得的大量数据既可以作为对舟山市海洋功能区划施行情况的响应,又将为舟山及其邻近海域浮游细菌群落结构的进一步研究奠定基础。     

Gut microbiomes of mobile predators vary with landscape context and species identity

Landscape context affects predator–prey interactions and predator diet composition, yet little is known about landscape effects on insect gut microbiomes, a determinant of physiology and condition. Here, we combine laboratory and field experiments to examine the effects of landscape context on the gut bacterial community and body condition of predatory insects. Under laboratory conditions, we found that prey diversity increased bacterial richness in insect guts. In the field, we studied the performance and gut microbiota of six predatory insect species along a landscape complexity gradient in two local habitat types (soybean fields vs. prairie). Insects from soy fields had richer gut bacteria and lower fat content than those from prairies, suggesting better feeding conditions in prairies. Species origin mediated landscape context effects, suggesting differences in foraging of exotic and native predators on a landscape scale. Overall, our study highlights complex interactions among gut microbiota, predator identity, and landscape context.