渤海沉积物中细菌群落结构和基因丰度的空间分布特征

This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were used to assay the bacterial 16S rRNA genes in the surface sediments of 13 sampling stations in the Bohai Sea.The results showed that sediments at the majority of the 13 sampling stations were contaminated by heavy metal mercury.The main phyla of bacteria recorded included Proteobacteria(52.92%),Bacteroidetes(11.76%),Planctomycetes(7.39%),Acidobacteria(6.53%)and Chloroflexi(4.97%).The genus with the highest relative abundance was Desulfobulbus(4.99%),which was the dominant genus at most sampling stations,followed by Lutimonas and Halioglobus.The main factors influencing bacterial community structure were total organic carbon,followed by depth and total phosphorus.The content of lead,cadmium,chromium,copper and zinc had a consistent effect on community structure.Arsenic showed a negative correlation with bacterial community structure in most samples,while the impact of mercury on community structure was not significant.The bacterial community in sediment samples from the Bohai Sea was rich in diversity and displayed an increase in diversity from high to low latitudes.The data indicated that the Bohai Sea had abundant microbial resources and was rich in bacteria with the potential to metabolize many types of pollutants.     

The ecology and phylogeny of cyanobacterial symbionts in sponges

Cyanobacteria have flexible photosynthetic apparatus that allows them to utilise light at very low levels, making them ideal symbionts for a wide range of organisms. Sponge associations with cyanobacteria are common in all areas of the world, but little is known about them. Recent research has revealed new cyanobacterial symbionts that may be host specific and two major clades, ' Candidatus Synechococcus spongiarum ' and Oscillatoria spongeliae , that occur in widely separated geographic locations in unrelated sponge hosts. These clades may represent a cluster of closely related symbiont species, or may be single species that are maintained by periods of horizontal transmission over large distances. Erroneous assumptions regarding the importance of cyanobacterial symbionts to the survival of individual sponges or species may arise from cyanosponges being deemed to be phototrophic or mixotrophic without studies of their photophysiology. This review brings together recent and past research on cyanobacterial associations with sponges, including their biogeography, phylogeny, host specificity, and ecology.     

Unexpected records of ‘deep‐sea’ carnivorous sponges Asbestopluma hypogea in the shallow NE Atlantic shed light on new conservation issues

Marine cave communities have been a continued source of ecological surprises, among other things because of their close ecological and evolutionary ties with the deep sea. The discovery of cladorhizid sponges, the deepest occurring poriferan family, in shallow Mediterranean caves in the 1990s was one such surprise, leading to the generally accepted hypothesis that the whole family was carnivorous, an unprecedented feeding mode for sponges. The recent observation of the cave species Asbestopluma hypogea in the Mediterranean bathyal, confirmed the view that some shallow caves can occasionally shelter otherwise deep‐dwelling species. Here we present new distribution data of A. hypogea, from deep Mediterranean locations, and for the first time from Atlantic locations. Among the new Atlantic records, the most surprising ones are located in three different geographic areas (Ria de Arousa, Groix Island and Cherbourg) of the NW European coasts, from the Iberian Peninsula to the English Channel, where A. hypogea reaches SCUBA depths (5–50 m), while not sheltered in marine caves. The carnivorous sponge however reaches its shallowest occurrence (5 m), in a small cave at Groix Island. The ecological significance of these discoveries, particularly the very patchy distribution and peculiar dynamics, are noteworthy, and the shallow occurrence of A. hypogea, together with other deep‐water or uncommon species, constitute unique assemblages that must be considered in conservation plans.     

The role of water mass dynamics in controlling bacterial abundance and production in the middle Adriatic Sea

Month-to-month fluctuations in the abundance of bacteria and heterotrophic nanoflagellates (HNF) and bacterial production, as well as various chemical (nutrients, oxygen) and physical (salinity, temperature) parameters were analysed at a station located in the open middle Adriatic Sea during one decade (1997-2006). Being influenced by both coastal waters and open Adriatic circulation in the surface layer, and by the deep Adriatic water masses in the deep layers (100 m), this station is quite suitable for detecting the environmental changes occurring in the open Adriatic Sea with respect to the circulation of its water masses and their long-term changes and anomalies. Multivariate methods were used to identify seasonal and inter-annual changes of the investigated parameters, associating observed changes to the changes in Adriatic water masses and circulation regimes. The analyses showed that bacterial abundance and production were controlled by different water mass dynamics during 1997-2001 compared to 2002-2006 period, particularly noticeable in different seasonal patterns of biological parameters. The interplay between North Adriatic Dense Water (NAdDW) and Levantine Intermediate Water (LIW) resulted in a change in the available nutrients (NAdDW is poor in orthophosphates), and as a consequence different bacterial abundance and production. A few periods were examined in detail, such as 2004, when LIW inflow was particularly strong and was accompanied by an increase of bacterial and HNF abundances, as well as of bacterial production.     

北黄海微表层细菌丰度与可培养细菌群落结构分析

为分析海洋微表层这一特殊生境中的细菌类群,于2010—2011年4个航次对北黄海微表层和次表层海水中的总菌丰度、可培养细菌丰度和群落结构进行了分析。采用流式细胞仪测定总菌丰度,平板计数法测定可培养细菌丰度,PCR-16SrDNA分析可培养细菌的群落结构。结果表明,调查海域微表层海水总菌均值为1.76×106 cell/mL,次表层海水总菌均值为1.07×106 cell/mL。可培养细菌丰度范围是1.00×102~1.70×106 CFU/mL,微表层和次表层可培养细菌所占总菌数量的百分比分别为13.05%和0.45%。微表层对总菌的富集因子(EF)均值为2.02,可培养细菌的EF均值为74.16。PCR-16SrDNA序列分析结果表明,该海域可培养细菌分属变形菌门(Proteobacteria)(94.34%)、厚壁菌门(Firmicutes)(1.89%)、拟杆菌门(Bacteroidetes)(1.89%)和放线菌门(Actinobacteria)(1.89%)4个类群。本研究初步发现,微表层对细菌具有较强的聚集作用,尤其对可培养细菌聚集作用更为明显。微表层中可培养细菌的群落结构与次表层有所不同,其种类丰富,来源和功能多样。由此可见,微表层独特的生境成就了其独特的微生物类群,其生态功能有待于进一步研究。     

两种黄海潮间带海绵的元素与氨基酸成分分析

应用能量色散X射线荧光光谱(EDXRF)分析了黄海潮间带繁茂膜海绵(Hymeniacidon perleve)和肾指海绵(Reniochalina sp.)的无机元素,其中硅是两种海绵中最多的无机元素。繁茂膜海绵较肾指海绵的锌含量高,参照文献数据推测这可能是该属海绵的特性。测定了2种海绵的含水量,有机碳、氮、氢元素和氯基酸在海绵干质量中的比例。分析了繁茂膜海绵在2002年8月到11月中主要无机元素的变化,发现繁茂膜海绵中的硅含量在降低。繁茂膜海绵的氨基酸总量远高于肾指海绵,2种海绵中含量较高的氨基酸是甘氨酸、谷氨酸、天冬氨酸、亮氨酸、缬氨酸、赖氨酸等。元素与氨基酸分析将对海绵细胞培养基开发有帮助。     

T-RFLP技术及其在微生物群落结构研究中的应用

微生物是生态系统的重要组成部分,在各种元素的生物地化循环中起关键作用。因此研究微生物的群落结构,借此了解微生物和环境的关系就尤为重要。长久以来微生物群落结构的调查方法一直是建立在分离和培养的方法上。这种方法不但费时费力,而且不够准确。这反映在如下几个方面：(1)微生物群落组     

施肥对盐沼沉积物微生物生物量和细菌群落组成的影响

The effects of nitrogen(N) addition on microbial biomass, bacterial abundance, and community composition in sediment colonized by Suaeda heteroptera were examined by chloroform fumigation extraction method, real-time quantitative polymerase chain reaction, and denaturing gradient gel electrophoresis(DGGE) in a salt marsh located in Shuangtai Estuary, China. The sediment samples were collected from plots treated with different amounts of a single N fertilizer(urea supplied at 0.1, 0.2, 0.4 and 0.8 g/kg(nitrogen content in sediment) and different forms of N fertilizers(urea,(NH_4)_2SO_4, and NH_4NO_3, each supplied at 0.2 g/kg(calculated by nitrogen).The fertilizers were applied 1–4 times during the plant-growing season in May, July, August, and September of 2013. Untreated plots were included as a control. The results showed that both the amount and form of N positively influenced microbial biomass carbon, microbial biomass nitrogen, and bacterial abundance. The DGGE profiles revealed that the bacterial community composition was also affected by the amount and form of N.Thus, our findings indicate that short-term N amendment increases microbial biomass and bacterial abundance,and alters the structure of bacterial community.     

Characterization of bacterial community structure in vestimentiferan tubeworm Ridgeia piscesae trophosomes

Terminal‐restriction fragment length polymorphisms (T‐RFLPs) were used to address the question whether there are multiple phylotypes of bacteria within the trophosome of the vestimentiferan tubeworm Ridgeia piscesae in addition to the known endosymbiont. Clone libraries were constructed to aid in the identification of the additional bacterial phylotypes. Individual R. piscesae specimens were collected from Juan de Fuca Ridge, Axial Caldera and Explorer Ridge, Magic Mountain. Clone library analyses revealed only one bacterial phylotype (expected R. piscesae endosymbiont) within the Explorer Ridge trophosomes. However, the Axial Caldera clone library revealed five operational taxonomic units (OTUs). Three of the resulting phylotypes detected (designated RAE) were putative thioautotrophic symbionts within the γ‐Proteobacteria which belonged to the anticipated endosymbiont group (RAE OTU 1), the Maorithyas hadalis symbiont II group (RAE OTU 3), and the Halothiobacillus group (RAE OTU 4). The remaining two phylotypes were most likely opportunistically derived. RAE OTU 5 was an α‐Proteobacterium within the Roseobacter group and RAE OTU 2 was within the Cytophaga–Flavobacterium–Bacteroidetes. T‐RFLP analyses revealed that all 15 trophosomes evaluated contained at least RAE OTUs 1 and 4. Five of the 15 trophosomes contained at least RAE OTUs 1, 3, and 4 and two of the trophosomes contained at least five RAE OTUs. Cluster analysis of the T‐RFLP data revealed three distinct clusters. The number of taxa within the trophosome may be an indication of the general health of the tubeworm. This study strongly suggests that we have discovered and identified more than one bacterial phylotype within the trophosome of vestimentiferan R. piscesae.     

Linking pollution induced community tolerance (PICT) and microbial community structure in chronically metal polluted estuarine sediments

We tested the ability of pollution induced community tolerance (PICT) to detect the effects of chronic metal pollution on estuarine sediment microbial communities, along a gradient spanning two orders of magnitude in metal concentrations. In tandem, we investigated the associated microbial community structure using terminal restriction fragment length polymorphism (T-RFLP). Tolerance of microbes to Cu, measured as IC50 (inhibitory concentration 50%), was strongly correlated with pore water Cu concentration (r(2)=0.842). No strong correlation existed for other metals tested, highlighting the ability of PICT to identify the pollutant causing a toxic effect. There was no correlation between microbial community structure and community tolerance to metals tested, but analysis of community structure did provide some information on reasons for observed PICT response. PICT methodology used here provided a greater strength and consistency of association with pollutant concentration compared to microbial community structure and can be recommended as a sensitive indicator of metal pollution on estuarine sediment microbial communities.     

南极纳尔逊冰川土壤中微生物的群落结构及其代谢特征研究

冰川土壤中的微生物是冰冻圈生态系统中的重要组成部分。南极纳尔逊冰川四周环海,临近海洋的物质输送和其他因素扰动改变了近岸土壤中部分理化因子,从而对土壤中的微生物群落产生影响。本研究采集了南极纳尔逊冰川不同近海距离处的土壤样品,并对其进行了细菌和古菌V4区扩增子测序以及宏基因组测序,探讨了不同近海距离的冰川土壤中的微生物群落结构和代谢潜能。物种多样性结果显示,不同位点的土壤微生物群落组成有所差异,但变形菌门、放线菌门、拟杆菌门等在冰川土壤样品中普遍存在且相对丰度较高。宏基因组分析结果显示,不同近海距离的冰川土壤微生物群落的功能基因分布不同,且能量代谢和跨膜运输等代谢途径的基因的丰度随着采样位点远离海洋而降低。冰川土壤中碳、氮、硫代谢分别以还原性柠檬酸循环、反硝化、同化硫酸盐还原途径为主,其中反硝化途径基因在所有样品中丰度较高。通过分箱组装获得了含有反硝化功能基因的基因组bin＿71,并重构了其核心的代谢通路。本研究初步揭示了南极纳尔逊冰川土壤中微生物的群落结构及代谢潜能,为后续南极冰川土壤新物种的发现、功能基因的挖掘、以及探究全球气候变暖下海洋对沿海生态系统的影响提供了基础数据。     

海绵和海鞘中可培养放线菌的分离与多样性比较

在相同的分离培养条件下,为比较地域差别较大的福建海域海绵动物(山海绵Mycale sp.和网架海绵Stylissa sp.)和海南海域海鞘动物(皱瘤海鞘Styela plicata和乳突皮海鞘Molgula manhattensis)之间可培养放线菌多样性的差异,作者采用5种放线菌分离培养基和1种细菌通用培养基,对海绵和海鞘中的放线菌进行分离培养。采用16S rRNA 基因限制性片段长度多态性(Restriction Fragment Length Polymorphism, RFLP)分析和序列分析,揭示其多样性。共获得可培养放线菌198株,其中从海绵中分离到87株放线菌,从海鞘中分离到111株放线菌。RFLP分析表现为38种不同的图谱类型。16S rRNA基因序列分析表明,从海绵中分离到的放线菌包括6个放线菌属,其中有2株菌的16S rRNA基因序列与最相近的菌株相似性低于97%,可能是潜在的新菌株;从海鞘中分离到的放线菌包括7个放线菌属,有8株可能是潜在的新菌株。比较海绵和海鞘中可培养放线菌的多样性发现,从海绵中分离到的放线菌,除节细菌(Arthrobacter)以外,均包括在海鞘分离的放线菌属中。海鞘相关放线菌多样性水平不容忽视,是除海绵之外另一获得新型放线菌资源以及药用天然活性产物的重要来源。     

Vertical changes in abundance,biomass and community structure of copepods down to 3000 m in the southern Bering Sea

Vertical changes in abundance, biomass and community structure of copepods down to 3000 m depth were studied at a single station of the Aleutian Basin of the Bering Sea (53°28′N, 177°00′W, depth 3779 m) on the 14th June 2006. Both abundance and biomass of copepods were greatest near the surface layer and decreased with increase in depth. Abundance and biomass of copepods integrated over 0–3000 m were 1,390,000 inds. m^?2 and 5056 mg C m^?2, respectively. Copepod carcasses occurred throughout the layer, and the carcass:living specimen ratio was the greatest in the oxygen minimum layer (750–100 m, the ratio was 2.3). A total of 72 calanoid copepod species belonging to 34 genera and 15 families occurred in the 0–3000 m water column (Cyclopoida, Harpacticoida and Poecilostomatoida were not identified to species level). Cluster analysis separated calanoid copepod communities into 5 groups (A–E). Each group was separated by depth, and the depth range of each group was at 0–75 m (A), 75–500 m (B), 500–750 m (C), 750–1500 m (D) and 1500–3000 m (E). Copepods were divided into four types based on the feeding pattern: suspension feeders, suspension feeders in diapause, detritivores and carnivores. In terms of abundance the most dominant group was suspension feeders (mainly Cyclopoida) in the epipelagic zone, and detritivores (mainly Poecilostomatoida) were dominant in the meso- and bathypelagic zones. In terms of biomass, suspension feeders in diapause (calanoid copepods Neocalanus spp. and Eucalanus bungii) were the major component (ca. 10–45%), especially in the 250–3000 m depth. These results are compared with the previous studies in the same region and that down to greater depths in the worldwide oceans.     

Collaboration among sponge species increases sponge diversity and abundance in a seagrass meadow

Caribbean sponge species typical of coral reefs are generally inhibited from living in seagrass meadows by their vulnerability to predation by the large starfish Oreaster reticulatus (Linnaeus 1758). Although readily consumed by Oreaster , the conspicuous coral reef sponge species Lissodendoryx colombiensis Zea & van Soest, 1986 has expanded its habitat distribution to include a seagrass ( Thalassia testudinum Banks ex König, 1805) meadow in Belize, where individuals grow to volumes of nearly 7 l. By simple observation, L. colombiensis appears to be an inferior competitor in this system, because portions of many individuals are overgrown by seagrass sponge species. However, experimentally clustering seagrass sponges around L. colombiensis individuals deterred starfish from feeding on them, suggesting an advantage to being overgrown. Sizes of individual L. colombiensis can fluctuate widely over short time intervals, reflecting both a relatively fast growth rate and the high rate at which starfish consume this species. At the population level these fluctuations are not evident, as losses of L. colombiensis due to Oreaster are balanced by a combination of efficient recruitment, rapid regeneration and growth, and protection of portions of many individuals by the overgrowth of seagrass sponge species that are unpalatable to Oreaster . In turn, the seagrass sponges acquire stable perches on L. colombiensis individuals in this sediment-dominated habitat. Community ecology theory relating to diversity patterns in sessile organisms has focused on competition between space-requiring neighbors as the underlying process that inevitably decreases diversity unless curtailed. Sponges, with their propensity for engaging in beneficial interactions with neighbors, demand expansion of the theory to acknowledge how collaboration can increase abundance and species diversity within a community.     

Plankton community and bacterial metabolism in Arctic sea ice leads during summer 2010

Microbial plankton metabolism was examined during summer 2010 in sea ice-influenced waters of the Fram Strait, eastern Arctic Ocean. Rates of gross primary production and community respiration were tightly coupled over a wide range of values (33±3–143±6 and 20±3–126±6 mmol O₂ m^{−2  −1}, respectively) leading to a prevalence of positive net community production. The high variability in community respiration, similar to that of gross primary production, suggests that heterotrophic metabolism may exhibit a significant response to environmental change. Bacterial respiration was assessed at similar time scales to bacterial production measurements, by determining the in vivo INT reduction capacity without pre-filtering the community. Bacteria seem to play a major role in total community respiration, contributing between 5% and 61% of total community respiration, indicating that a high fraction of the organic carbon in Arctic planktonic food webs could flow through these microbes.     

Temperature‐ and size‐associated differences in the skeletal structures and osculum cross‐sectional area influence the pumping rate of contractile sponge Cinachyrella cf. cavernosa

Sponges alter the proportion of structural and morphological components such as spicule skeleton and number of oscula in response to environment, development and growth. Such mechanisms indicate morphological and physiological variations within populations. We measured the pumping rate of different sized specimens of contractile sponge Cinachyrella cf. cavernosa present in the intertidal rock pools, during morning and afternoon low tides along the central west coast of India. Additionally, we measured the exhalant opening (oscular cross‐sectional area—OSA), tissue density, spicule skeleton weight and the abundance of choanocyte chambers to assess the morphological variations. Water temperature and sponge size showed a significant positive effect on pumping rate. OSA and the number of oscula increased with sponge size, but the sponge volume‐specific pumping rate did not increase (0.029 ± 0.020 ml/s ml^‐1). Histological sections showed the abundance of chaonocyte chambers increased marginally with the sponge size, but the contraction state affected the count. Both tissue density and spicule skeleton weight were positively correlated with sponge size, particularly the increase in the size and number of spicule bundles radiating from the centre indicated a denser core in larger specimens. The subcortical lacunae and the peripheral choanosome with high abundance of canals appear to be the major volume reduction zones during contraction events. Our results indicate that the size and number of spicule bundles increase with sponge volume and the variation in temperature, contraction state, and size and number of oscula influence the pumping rate of C. cf. cavernosa.     

Habitat modification in tidepools by bioeroding sea urchins and implications for fine‐scale community structure

By creating novel habitats, habitat‐modifying species can alter patterns of diversity and abundance in marine communities. Many sea urchins are important habitat modifiers in tropical and temperate systems. By eroding rocky substrata, urchins can create a mosaic of urchin‐sized cavities or pits separated by exposed, often flat surfaces. These microhabitats appear to harbor distinct assemblages of species. We investigated how a temperate rocky intertidal community uses three small‐scale (<100 cm²) microhabitats created by or adjacent to populations of the purple sea urchin (Strongylocentrotus purpuratus): pits occupied by urchins, unoccupied pits, and adjacent flat spaces. In tidepools, flat spaces harbored the highest percent cover of algae and sessile fauna, followed by empty pits and then occupied pits. The Shannon diversity and richness of these sessile taxa were significantly higher in flat spaces and empty pits than in occupied pits. The composition of these primary space holders in the microhabitats also varied. Unlike primary space holders, mobile fauna exhibited higher diversity and richness in empty pits than in flat spaces and occupied pits, although results were not significant. The protective empty pit microhabitat harbored the highest densities of most trophic functional groups. Herbivores, however, were densest in flat spaces, concordant with high algal coverage. These results suggest the habitats created by S. purpuratus in addition to its biological activities alter community structure at spatial scales finer than those typically considered for sea urchins.     

Biodiversity,ecological structure,and change in the sponge community of different geomorphological zones of the barrier fore reef at Carrie Bow Cay,Belize

Changes in the relative abundance of benthic groups on the barrier fore reef at Carrie Bow Cay, Belize, point to a significant reduction of corals and an expansion of the sponge community in 1995–2009. Fifty‐one species are now present in the four geomorphological zones of this reef: the low‐relief spur‐and‐groove zone, the inner reef slope, the outer ridge, and the fore‐reef slope (to a depth of 30 m). Five species are new additions to the sponge fauna reported for Belize, and six species account for 42.6% of the total assemblage: Niphates erecta (9.60%), Aiolochroia crassa (8.8%), Niphates digitalis (6.9%), Callyspongia plicifera (6.63%), Aplysina archeri (5.37%) and Xestospongia muta (5.37%). Species richness, average density, diversity and evenness indexes are statistically similar in these four zones but some species appear to be more dominant in certain areas. In the same 30 years, coral cover has decreased by more than 90%, while the octocoral cover has greatly increased (by as much as 10‐fold in the low‐relief spur‐and‐groove zone). Thus the Carrie Bow fore reef appears to be undergoing a transition from coral dominance in the late 1970s to algae dominance today, with other benthic groups such as sponges and octocorals showing signs of gradual recovery.