Soil microbial community analysis using denaturing gradient gel electrophoresis

The most biological diversity on this planet is probably harbored in soils. Understanding the diversity and function of the microbiological component of soil poses great challenges that are being overcome by the application of molecular biological approaches. This review covers one of many approaches being used: separation of polymerase chain reaction (PCR) amplicons using denaturing gradient gel electrophoresis (DGGE). Extraction of nucleic acids directly from soils allows the examination of a community without the limitation posed by cultivation. Polymerase chain reaction provides a means to increase the numbers of a target for its detection on gels. Using the rRNA genes as a target for PCR provides phylogenetic information on populations comprising communities. Fingerprints produced by this method have allowed spatial and temporal comparisons of soil communities within and between locations or among treatments. Numerous samples can be compared because of the rapid high throughput nature of this method. Scientists now have the means to begin addressing complex ecological questions about the spatial, temporal, and nutritional interactions faced by microbes in the soil environment.

Enrichment of the hydrogen-producing microbial community from marine intertidal sludge by different pretreatment methods

To determine the effects of pretreatment on hydrogen production and the hydrogen-producing microbial community, we treated the sludge from the intertidal zone of a bathing beach in Tianjin with four different pretreatment methods, including acid treatment, heat-shock, base treatment as well as freezing and thawing. The results showed that acid pretreatment significantly promoted the hydrogen production by sludge and provided the highest efficiency of hydrogen production among the four methods. The efficiency of the hydrogen production of the acid-pretreated sludge was 0.86 +/- 0.07 mol H-2/mol glucose (mean +/- S.E.), whereas that of the sludge treated with heat-shock, freezing and thawing, base method and control was 0.41 +/- 0.03 mol H-2/mol glucose, 0.17 +/- 0.01 mol H-2/mol glucose, 0.11 +/- 0.01 mol H-2/mol glucose and 0.20 +/- 0.04 mol H-2/mol glucose, respectively. The result of denaturing gradient gel electrophoresis (DGGE) showed that pretreatment methods altered the composition of the microbial community that accounts for hydrogen production. Acid and heat pretreatments were favorable to enrich the dominant hydrogen-producing bacterium, i.e. Clostridium sp., Enterococcus sp. and Bacillus sp., However, besides hydrogen-producing bacteria, much non-hydrogen-producing Lactobacillus sp. was also found in the sludge pretreated with base, freezing and thawing methods. Therefore, based on our results, we concluded that, among the four pretreatment methods using acid, heat-shock, base or freezing and thawing, acid pretreatment was the most effective method for promoting hydrogen production of microbial community. (C) 2009 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.

Community structure and seasonal dynamics of planktonic ciliates along salinity gradients

The ciliate community structure and seasonal dynamics in a solar saltern of the Yellow Sea were studied based oil 4 sampling dates and 8 stations with salinities from 27.7 parts per thousand to 311.0 parts per thousand. The effects of the type and concentration of the fixative used (Lugol's and Bouin's) were tested at the first sampling date. Fixative type and fixative concentration had significant effects on ciliate abundance and blovolume, with 1% Lugol's giving the best results. A detailed investigation using live observations and protargol staining techniques revealed a total of 98 morphospecies from 8 sampling stations. There was obvious seasonal variation in species composition at most of the stations, but this tended to be less distinct with increasing salinity, as the dominant ciliate group shifted from oligotrichs to heterotrichs. Ciliate abundance varied from 4.40 x 10(1) to 2.11 x 10(5) cells l(-1) and biomass ranged between 2.39 and 9.87 x 10(3) mu g Cl-1 (at a salinity of 147.6 parts per thousand). Both abundance and biomass decreased abruptly when salinity exceeded 100-150 parts per thousand. Statistical analyses Suggested that the dynamics of ciliate abundance and biomass were regulated by both salinity and by season, but those of diversity and species richness were mainly controlled by salinity and both significantly decreased with increasing salinity. (C) 2009 Elsevier GmbH. All rights reserved.

Community structure of macrobenthos in coastal water off Rushan, southern Shandong Peninsula, and the relationships with environmental factors

To understand the present actuality of the marine ecosystem in the southern coastal water region of the Shandong Peninsula and the impact of the global change and the human activities to the marine ecosystem of the region, the macrobenthic community structure was researched based on data from 26 sampling stations carried out on four seasonal cruises from December 2006 to November 2007. The data was analyzed using PRIMER 6.0 and SPSS 15.0 software packages. The results showed that 236 macrobenthic species in total were collected from the research region by the field works. Most of the species belong to Polychaeta (76 species), Mollusca (75) and Crustacea (60). Of which, 33 species were common species by the four cruises. The dominant species were different among the four seasons, however, the polychaete species Nephtys oligobranchia and Sternaspis scutata were always dominant in the four seasons. The abundances and biomasses of the macrobenthos from the research region were variable in tire four seasons. The results of CLUSTER and MDS analysis showed that the similarities of macrobenthic structures among the stations were low, most of the similarities were at about 40% of similarity values, only that of two stations were up to 60%. In accordance with the similarity values of the macrobenthic structures, the 26 stations were clustered as six groups at arbitrary similarity level of 30%. The ABC curve indicated that the marcofauna communities in the research region had riot been disturbed distinctly. The results of BIOENV and BVSTEP (Spearman) analysis implied that the concentrations of organic matter in bottom water and heavy metal copper in sediment, water depth and temperature of bottom were the most significant environmental factors to affect the macrobentic community.

Summertime community structure of intertidal macrobenthos in Changdao Archipelago, Shandong Province, China

The community structure of intertidal macrobenthos in Changdao Archipelago (north of Shandong Peninsula, between Bohai Bay and the northern Yellow Sea) was examined based on samples collected from 14 stations in five transects in June 2007. Three stations corresponding to high, medium and low tidal areas were set up for each transect. A total of 68 macrobenthic species were found in the research region, most of which belonged to Mollusca and Crustacea. The average abundance and biomass of the macrobenthos was 1383 ind./m(2) and 372.41 g/m(2), respectively. The use of an arbitrary similarity level of 20% resulted in identification of five groups among the 14 stations in the research region. There were remarkable differences in the biomass, abundance and Shannon-Wiener diversity index of the different sediments. Specifically, the order of biomass was rocky shores > gravel > mud-sand > coarse sand > stiff mud, while the order of abundance was rocky shores > coarse sand > mud-sand > gravel > stiff mud, and that of the diversity index was mud-sand > gravel > stiff mud > rocky shores > coarse sand. The above results revealed that the sediment type was the most important factor affecting the structure of the macrobenthic community of the intertidal zone.

Macrobenthic community structure in the Changjiang Estuary and its adjacent waters in summer

On the basis of data collected in the summer of 2006 from 27 sampling stations in the Changjiang Estuary and its adjacent waters, the ecological characteristics of macrobenthos and the relationship between the macrobenthos and the environmental factors were studied using hierarchical cluster and non-metric multidimensional scaling ( MDS). The biomass, abundance, Shannon - Wiener's and Margalef' s indices of the macrobenthos were presented. The results showed that a total of 253 maerobenthic species were found in the research region, and most. of them belong to mollusks and polychaetes. The dominant species were Cossurella dimorpha, Eocylichna cylindrella, Episiphon kiaochowwanense, Nassarius semiplicatus, Ocstergrenia variabilis and Sternaspis scutata. The average abundance of the macrobenthos was (313.15 +/- 233.4) ind. / m(2), and the average biomass was (15.2 +/- 11.2) g/ m(2). The distribution patterns of the abundance and biomass of the macrobenthos were similar. The abundance and biomass in the area close to the estuary were lower than those from the area more distant to the estuary; the central part of the research region had higher abundance and biomass than other parts of the research region. In accordance with the results, four macrobenthic communities with distinct spatial differences were identified. The low abundance and biomass in the area close to the estuary should be caused by the high sedimentation rate. The statistical analysis indicated that the depth is the most important factor affecting the distribution of macrobenthos.

Effects of micronutrients on biological treatment efficiency of textile wastewater

Micronutrients play a very important role in biological processes for wastewater treatment. Many industrial wastewaters lack in nutrients (macronutrients and micronutrients) required for microbial growth, and this is one of the main problems at many activated sludge plants treating industrial wastewater. The microbial community structure is one of the important factors controlling the pollutant-degrading capacity of biological wastewater treatment system. In this study, the concentrations of micronutrients of the textile wastewater discharged from a textile plant were determined, and the effects of micronutrients on treatment efficiency and microorganism community structure of the biological treatment system were studied. The results showed that the optimal concentrations of magnesium, molybdenum, zinc, thiamine and niacin in the textile wastewater were 5.0, 2.0, 1.0, 1.0 and 1.0mg/L, respectively. The COD removal rates when magnesium, molybdenum, zinc, thiamine and niacin were added individually to the wastewater in their optimal concentrations were 1.8, 1.4, 1.3, 1.6 and 2.2 times of that of the control, respectively. The improving effects of combinations of zinc and thiamine, zinc and niacin, thiamine and niacin were better than single micronutrient. The diversity of quinones (DQ) changed significantly after the micronutrient was added into the wastewater treatment system. This indicated that there was probably a feasibility of optimizing the biological treatment performances and microorganism community structure of textile wastewater treatment system through micronutrient supplement.

大气氮沉降增加对土壤微生物群落结构和土壤酶活性的影响

大气无机氮沉降因人类活动的加剧增加了多倍，虽然增加的N给森林生态系统带来了一定的肥力效应，但从长远来看，过量的氮沉降会对生物化学循环、土壤理化性质和森林生产力产生负作用。目前大多数研究都集中在氮沉降对土壤化学和C、N循环的影响，而对调节土壤生态系统过程中起关键作用的土壤酶和土壤微生物却知之甚少。 本文选择长白山地区天然阔叶红松林和天然次生杨桦林为研究对象，控制人工施氮量：对照（0 kg N•ha-1•yr-1）、低氮（25 kg N•ha-1•yr-1）和高氮（50 kg N•ha-1•yr-1），通过对表层土壤中土壤微生物磷脂脂肪酸(PLFA)和几种土壤酶活性的定量测定及分析，探索不同施氮条件下土壤微生物群落及土壤酶活性的变化情况。结果表明： （1）大气氮沉降增加显著影响土壤酶（纤维素酶、蔗糖酶和多酚氧化酶）活性，并且因林分类型、施氮强度与时间表现各异。氮沉降增加显著降低了阔叶红松林土壤多酚氧化酶活性(P<0.05)；高氮处理对杨桦林土壤纤维素酶活性表现出抑制现象；杨桦林中蔗糖酶活性随施氮量的增加而降低，红松林中酶活随施氮量的增加而升高。 （2）土壤微生物量对氮沉降的响应因植被的不同而异，杨桦林中土壤微生物量C降低，而阔叶红松林中微生物量C则升高。微生物C:N在两种林型中表现相同，均略有升高。 （3）不同林型和不同树木生长期内微生物群落对氮沉降的响应差异较大。生长季初期（5月），高氮沉降导致细菌/真菌比降低，各类微生物的PLFA量减少，两种林分类型表现相同；生长季中期（7月），高氮沉降使细菌/真菌比升高，但微生物群落的变化在两种林型中有所不同，杨桦林中高氮沉降使细菌、真菌和放线菌的PLFA量都减少，而阔叶红松林中各类微生物的PLFA量都有所增加。 （4）氮沉降增加条件下，阔叶红松林中，纤维素酶、多酚氧化酶和蔗糖酶活性和真菌数量呈显著负相关，但在杨桦林中三种酶活性和微生物无相关关系。

OLAND生物脱氮系统运行条件及其微生物群落结构的研究

OLAND两阶段生物脱氮系统是一项正在开发且极具应用前景的处理高氨氮、低COD废水的新技术。在实验室水平，对OLAND系统限氧亚硝化阶段MBR反应器和厌氧氨氧化阶段SBR反应器的启动和运行进行了系统研究。MBR反应器控制参数在DO0.1-0.3mg/L，pH7.8±0.1，温度30±0.5℃，SRT无穷大的条件下，可实现在较高的容积负荷By＝IO00mgN／L，水力停留时间HRT：ld下稳定的亚硝酸型硝化，使NH4+-N和NO2-N的出水比例达到理想的比值（1:1.20±0.20），保证厌氧氨氧化阶段SBR反应器的理想进水；SBR反应器在完全厌氧、pH7.8-8.2，温度30±0．5℃，SRT无穷大的条件下，无需外加任何有机碳源，在较高总氮负荷550mgN／L下，可实现NH4+-N和NO2--N同时稳定的去除，二者的消耗比例为1:（1.21±0.05），总氮去除率高达92％。采用巢式PCR、DGGE、 FISH等分子技术对MBR反应器硝化菌群随溶解氧的动态变化规律和SBR反应器厌氧氨氧化菌群结构、组成进行了研究，并探讨了硝化菌群与氮素组成变化之间的内在联系。结果表明：在限氧亚硝化阶段硝化菌群中氨氧化菌受溶解氧浓度的影响较大，其种群结构从反应器启动初期到稳定后期发生了非常明显的变化。亚硝酸氧化菌NOB的种群组成受溶氧影响并不明显，从启动初期到稳定后期其种群结构无明显变化。硝化菌群中氨氧化菌 AOB与亚硝酸氧化菌NOB的数量比例关系随溶解氧的降低而不断升高，从最初的3.6:1升高到稳定后期的5.5:1。MBR反应器优势硝化菌群主要由A、B、C三类氨氧化菌和硝化杆菌D、硝化螺菌F组成，其中优势菌C为维持MBR反应器稳定出水比例的主要功能菌。硝化菌群组成和结构的变化，带来了不同N素之间组成和比例的规律性变化。厌氧氨氧化阶段基本由厌氧氨氧化菌AnAOB和ANAMMOX两类菌组成，二者空间结构紧密，在反应器中的活菌数量比例分别为55％和42％。厌氧氨氧化菌AnAOB种群多样性相对比较丰富，主要由条带I和H所代表的两种优势菌组成；ANAMMOX菌种群多样性变化较小，其种群主要由优势菌K和J组成。对MBR和SBR反应器中的优势菌进行了克隆、测序和系统发育学分析，结果表明：限氧亚硝化阶段MBR反应器启动初期的优势菌A属于Nitrosomonadaceae科，是否是一个新属，还有待于进一步鉴定。运行中期优势菌B与Nitroso）nonaseurooaea亲缘关系最近，同源性高达99.1％，暂命名为Nilrosomonas sp.BI。稳定后期优势菌C与Nitrosomonas eutroPha亲缘关系最近，同源性为96.3％，暂命名为Nifrosomonas sp．cl。硝化杆菌属优势菌D与Nitrobacter alkalicus、Nitrobacter hambllrgensts和Nitlobac招rwinograsky 亲缘关系较近，同源性分别为95.5-97％、96.5～97％和95.8～96.8％。SBR反应器中AnAOB优势菌I与MBR反应器优势菌B亲缘关系最近，同源性高达98.7％，与Nitlosomonas euroPaea同源性为98.3％。根据序列比较和生理特性分析，优势菌I与优势菌B应为Nitrosomonas属两个不同的种，暂将优势菌I命名为Nitrosomonas sp．II。优势菌H与MBR反应器优势菌C亲缘关系最近，同源性达97.9％，与Nitrosomonas eutropha同源性为96.3％。结合其生理特性分析，二者应为Nitrosomonas属两个不同的种，暂将优势菌H命名为Nitrosomollas sp．Hl。ANAMMox优势菌K与未培养的 Planctomycete和已鉴定的另一种ANAMMoX菌尤uenenia sf况ttgartiensis亲缘关系较近，同源性分别为99.8％和96.6％。优势菌J与Gen bank收录的所有菌的相似性均低于76％，说明该菌是OLAND系统厌氧氨氧化阶段比较独特的菌，是迄今为止在厌氧反应过程中未发现的一个新菌。

Close coupling between phytoplankton growth and microzooplankton grazing in the western South China Sea

We conducted 28 dilution experiments during August-September 2007 to investigate the coupling of growth and microzooplankton grazing rates among ultraphytoplankton populations and the phytoplankton community and their responses to habitat variability (open-ocean oligotrophy, eddy-induced upwelling, and the Mekong River plume) in the western South China Sea. At the community level, standing stocks, growth, and grazing rates were strongly and positively correlated, and were related to the higher abundance of larger phytoplankton cells (diatoms) at stations with elevated chlorophyll concentration. Phytoplankton growth rates were highest (> 2 d(-1)) within an eastward offshore jet at 13 degrees N and at a station influenced by the river plume. Among ultraphytoplankton populations, Prochlorococcus dominated the more oceanic and oligotrophic stations characterized by generally lower biomass and phytoplankton community growth, whereas Synechococcus became more important in mesotrophic areas (eddies, offshore jet, and river plume). The shift to Synechococcus dominance reflected, in part, its higher growth rates (0.87 +/- 0.45 d(-1)) compared to Prochlorococcus (0.65 +/- 0.29 d(-1)) or picophytoeukaryotes (0.54 +/- 0.50 d(-1)). However, close coupling of microbial mortality rates via common predators is seen to play a major role in driving the dominance transition as a replacement of Prochlorococcus, rather than an overprinting of its steady-state standing stock.

Seasonal change in the structure of fig-wasp community and its implication for conservation

Figs (Moraceae) and their pollinating wasps (Agaonidae) constitute a famous reciprocal mutualism in which figs provide some female flowers for the development of fig wasp offspring while the fig wasps pollinate Fig flowers. However, figs also host many no