Species Diversity of Uncultured and Cultured Populations of Soil and Marine Ammonia Oxidizing Bacteria

Although molecular techniques are considered to provide a more comprehensive view of species diversity of natural microbial populations, few studies have compared diversity assessed by molecular and cultivation-based approaches using the same samples. To achieve this, the diversity of natural populations of ammonia oxidising bacteria in arable soil and marine sediments was determined by analysis of 16S rDNA sequences from enrichment cultures, prepared using standard methods for this group, and from 16S rDNA cloned from DNA extracted directly from the same environmental samples. Soil and marine samples yielded 31 and 18 enrichment cultures, respectively, which were compared with 50 and 40 environmental clones. There was no evidence for selection for particular ammonia oxidizer clusters by different procedures employed for enrichment from soil samples, although no culture was obtained in medium at acid pH. In soil enrichment cultures, Nitrosospira cluster 3 sequences were most abundant, whereas clones were distributed more evenly between Nitrosospira clusters 2, 3, and 4. In marine samples, the majority of enrichment cultures contained Nitrosomonas, whereas Nitrosospira sequences were most abundant among environmental clones. Soil enrichments contained a higher proportion of identical sequences than clones, suggesting laboratory selection for particular strains, but the converse was found in marine samples. In addition, 16% of soil enrichment culture sequences were identical to those in environmental clones, but only 1 of 40 marine enrichments was found among clones, indicating poorer culturability of marine strains represented in the clone library, under the conditions employed. The study demonstrates significant differences in species composition assessed by molecular and culture-based approaches but indicates also that, employing only a limited range of cultivation conditions, 7% of the observed sequence diversity in clones of ammonia oxidizers from these environments could be obtained in laboratory enrichment culture. Further studies and experimental approaches are required to determine which approach provides better representation of the natural community.     

Influence of Land Use Intensity on the Diversity of Ammonia Oxidizing Bacteria and Archaea in Soils from Grassland Ecosystems

In the present study, the influence of the land use intensity on the diversity of ammonia oxidizing bacteria (AOB) and archaea (AOA) in soils from different grassland ecosystems has been investigated in spring and summer of the season (April and July). Diversity of AOA and AOB was studied by TRFLP fingerprinting of amoA amplicons. The diversity from AOB was low and dominated by a peak that could be assigned to Nitrosospira. The obtained profiles for AOB were very stable and neither influenced by the land use intensity nor by the time point of sampling. In contrast, the obtained patterns for AOA were more complex although one peak that could be assigned to Nitrosopumilus was dominating all profiles independent from the land use intensity and the sampling time point. Overall, the AOA profiles were much more dynamic than those of AOB and responded clearly to the land use intensity. An influence of the sampling time point was again not visible. Whereas AOB profiles were clearly linked to potential nitrification rates in soil, major TRFs from AOA were negatively correlated to DOC and ammonium availability and not related to potential nitrification rates.     

Higher Abundance of Ammonia Oxidizing Archaea than Ammonia Oxidizing Bacteria and Their Communities in Tibetan Alpine Meadow Soils under Long-term Nitrogen Fertilization

Increasing usage of nitrogen fertilizer for food production has resulted in severely environmental problems of nutrients enrichment. This study aimed to examine the response of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) to a long-term nitrogen fertilization in Tibetan alpine meadow. The abundance and composition of both AOB and AOA were assessed using quantitative real-time PCR, cloning and sequencing techniques based on amoA gene under different fertilization gradient (0, 30, 60, 90, and 120 g m^?2 year^?1). Our results showed that, abundances of AOA amoA genes (ranging from 1.48 × 10⁹ to 2.00 × 10⁹ copies per gram of dry soil) were significantly higher than those of AOB amoA genes (1.25 × 10⁷ to 2.62 × 10⁸ copies per gram of dry soil) under fertilization scenario. The abundance of AOB amoA genes increased with increasing nitrogen fertilization, whereas fertilization had little effect on AOA abundance. Sequences of clone libraries of the different treatments revealed that AOB communities were dominated by representatives of Cluster 4, constituting 48.94–64.44% in each clone library. Sequences of Clusters 9, 1 and 2 were prevalent in soils under higher fertilization. All archaeal amoA sequences recovered were affiliated with the soil/sediment clade and marine sediment clade, and no significant difference was observed on the community structure among different fertilization treatments. Variations in the AOB community structure and abundance were linked to ammonium-N and soil pH induced by different fertilization treatments. These results showed that the abundance and structure of the AOB community respond to the fertilization gradient, not AOA.     

拉鲁湿地主要植物群落结构及物种多样性

2002年6~9月对拉鲁湿地植物种类、群落结构、生物量以及物种多样性进行了调查研究.结果表明:(1)拉鲁湿地共有植物30科52属85种,主要有芦苇[Phragmites australis(Cav.)Trin.ex Steud.](A)、尼伯尔酸模(RumexnepalensisSpreng)(B)、水葱(Scirpus validusVahl)(C)、穗状狐尾藻(MyriophyllumspicatumL.)(D)、灯芯草(Juncus effususL.)(E)、针叶苔草(CarexonoeiFranch.et Sav.)和黑褐苔草(CarexatrofuscaSchkuhr)(F)、藏北嵩草(KobresialittledaleiC.B.Clarke)(G)、藏蓟[Cirsiumlanatum(Roxb.ex Willd.)Spreng.](H)等8个主要植物群落.(2)在8个主要植物群落中,嵩草群落所含物种数最多,为44种,穗状狐尾藻群落最少,仅8种;芦苇群落生物量最高,为124.5~1 027.0 g/m2,藏蓟群落生物量最低,为124.5~220.5 g/m2;优势种芦苇的生物量最高,为183.5~660.0 g/m2,藏蓟生物量最低,为43.1~76.3 g/m2.(3)各群落的垂直结构特点是:芦苇群落、水葱群落、穗状狐尾藻群落具有挺水层、浮叶层和沉水层,其他群落只具有可分为高、低两层的草本层.(4)在各群落的相似性方面,嵩草群落与藏蓟群落、水葱群落与芦苇群落和尼伯尔酸模群落的相似性要明显高于其他群落,其Jaccard系数分别为0.549 0、0.538 5、0.500 0;芦苇群落、尼伯尔酸模群落、水葱群落、穗状狐尾藻群落与藏蓟群落以及芦苇群落、穗状狐尾藻群落与嵩草群落在建群种上没有相似之处,Jaccard系数为0.     

Microbial Population and Activity in Wetland Microcosms Constructed for Improving Treated Municipal Wastewater

The idea of using constructed wetlands for the treatment and improving of wastewater emerged in the second half of the last century. Despite relatively wide use of this environmentally friendly technology, relatively little is known about the microbial populations involved in biotransformation and removal of contaminants in this system. The aim of the current study was to investigate the assembly and function of microbial populations in vertical-flow constructed wetland microcosms designed to improve the quality of wastewater after activated sludge treatment. Also, the performance of 3-year-old wetland ponds was investigated. Even though the quality of the influent water was relatively high, improvement in water parameters such as coliform level, ammonia concentration, BOD, and TSS was observed. The performance of the wetland ponds was comparable to that of the microcosms. The microbial community composition of the biofilm formed on the surface of gravel particles in vegetated and plant-free microcosms was studied by denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene fragments. Highly complex bacterial diversity was observed in the biofilm. Cluster analysis of DGGE patterns demonstrated that depth within the wetland microcosm has a stronger effect on microbial community composition of the biofilm formed on wetland matrix than vegetation. Measurements of fluorescein diacetate hydrolysis activity and nitrification potential revealed that hydrolytic activity was affected by both microcosm depth and vegetation presence, whereas nitrification potential was mostly influenced by depth. Resolving the bacterial assemblage of wetland biofilm, which often is considered a black box, will help to understand the interactions involved in the development of diverse and mature biofilm and its function.     

甘南高寒草甸退化对植物功能群多样性与物种多度分布的影响

为分析甘南高寒草甸植物功能群多样性及其物种多度分布对退化的响应,探讨其多样性的形成与维持机制,采用样地调查法收集数据,并使用物种多度模型对其进行拟合分析。结果表明:随着退化程度的加深,植被优势种以禾草科和莎草科植物为主,逐渐变为杂草功能群植物为主,杂草功能群在群落多样性分布中起着主导作用;全部物种多度分布随着退化程度的加深发生变化,其中,无退化草甸的最优拟合模型是VOLKOV,轻度退化草甸的最优拟合模型是GEO,中度退化草甸和重度退化草甸的最优拟合模型为BRO,资源分配模式由随机分配转向固定分配的分配模式;禾草功能群的最优拟合模型以生态位模型为主,资源分配方式由固定分配和随机分配共同主导,豆科功能群的最优拟合模型是BRO,资源分配方式以固定分配为主,杂草功能群的最优拟合模型从中性模型向生态位模型转变,与全部物种多度分布的最优模型基本一致,且资源分配由随机分配向固定分配转变,可以认为杂草功能群是影响群落物种多度分布的主要原因,但是禾草和豆科功能群的贡献也不可忽视。     

硫酸盐还原菌的分离纯化方法

硫酸盐还原菌在硫元素的地球生物循环及环境保护中都发挥着重要作用。介绍了硫酸盐还原菌的分离与纯化的方法,比较了厌氧袋、厌氧罐、厌氧工作站、厌氧管等方法的应用,以及在使用中需要注意的问题;同时介绍了分子生物学技术在硫酸盐还原菌分离纯化方面的应用,旨在为硫酸盐还原菌的分离纯化提供一定的参考依据。     

Effects of Arbuscular Mycorrhizas on Ammonia Oxidizing Bacteria in an Organic Farm Soil

Arbuscular mycorrhizal fungi (AMF) are potentially important in nutrient cycling in agricultural soils and particularly in soils managed for organic production; little is known, however, about the interrelationships between AMF and other members of soil microbial communities. Ammonia oxidizing bacteria (AOB) are a trophic group of bacteria having an enormous impact on nitrogen availability in soils and are expected to be influenced by the presence of AMF. In a field study, we utilized a unique genetic system comprised of a mycorrhiza defective tomato mutant (named rmc) and its mycorrhiza wild-type progenitor (named 76RMYC+). We examined the effect of AMF by comparing AOB community composition and populations in soil containing roots of the two tomato genotypes in an organically managed soil. Responses of AOB to soil N and P amendments were also studied in the same experiment. Phylogenetic analysis of cloned AOB sequences, derived from excised denaturing gradient gel electrophoresis (DGGE) bands, revealed that the organic farm soil supported a diverse yet stable AOB community, which was neither influenced by mycorrhizal colonization of roots nor by N and P addition to the soil. Real-time TaqMan polymerase chain reaction (PCR) was used to quantify AOB population sizes and showed no difference between any of the treatments. An alternative real-time PCR protocol for quantification of AOB utilizing SYBR green yielded similar results as the TaqMan real-time PCR method, although with slightly lower resolution. This alternative method is advantageous in not requiring the detailed background information about AOB community composition required for adaptation of the TaqMan system for a new soil.     

人工湿地中降解有机污染物细菌的分离筛选

采用平板划线法从人工湿地污水处理系统底泥和污水中分离出 2 3株细菌 ,在实验室条件下检测了这些细菌对灭菌污水和自然污水CODcr的去除效果 ,结果表明其中 8株细菌 (DN -4、DN -5、DN- 6、DN -10、DN -11、DN -12、DN- 13、WS- 5 )对灭菌污水和自然污水的CODcr均有较高的去除率 ,胞外酶检测表明该 8株细菌均能产生淀粉酶和接触酶 ,这些细菌具有潜在的应用价值。     

Abundance and Diversity of Glacial Bacteria on the Tibetan Plateau with Environment

The relation of glacial microorganism and their living environment is concerned but less understood for both glaciologists and microbiologists. Here we present the results about glacial snow bacteria from 3 glaciers on the Tibetan Plateau. The concentrations and diversity of bacteria collected from snow pit samples of East Rongbuk, Laohugou and Hailuogou glaciers on the Tibetan Plateau were investigated by epifluorescence microscope, denaturing gradient gel electrophoresis and Shannon-Weaver index. Concentrations and community diversity of bacteria in the East Rongbuk glacier with lower concentration and smaller size of microparticle were lower than in the Laohugou with higher concentration and larger size of microparticle. Bacterial concentration in East Rongbuk Glacier was close to that in polar regions, suggesting that Mt. Everest is a bacterial background for remote regions away from direct influence of anthropogenic sources. In addition, altitude difference was another factor for higher concentrations and community diversity of bacteria in Hailuogou and Laohugou glaciers than in East Rongbuk Glacier. The highest concentrations and community diversity of bacteria in Hailuogou Glacier were attributed to its most diverse atmospheric circulations and highest temperature among the 3 glaciers. We suggest a complicated correlation between glacial bacteria and their regional living environments.     

Species Abundance and Diversity of Burkholderia cepacia Complex in the Environment

Despite considerable interest in studying Burkholderia cepacia complex in the environment, we still do not have efficient methods to detect, isolate, and screen large numbers of B. cepacia isolates. To better describe the ecology and diversity of B. cepacia complex, a colony hybridization assay was developed to detect specifically all species of the complex based on polymorphism of the variable V3 region of the 16S rRNA sequence. The sensitivity of the assay was dramatically enhanced by using a probe consisting of three repeats of a B. cepacia complex-specific probe, each separated by a phosphoramidite spacer. In addition, a duplex PCR targeting B. cepacia complex-specific recA and 16S rRNA sequences was developed to enable a fast and reliable diagnostic assay for members of the complex. When applied to maize rhizosphere samples, colony hybridization results were in good agreement with those of most-probable-number duplex PCR, both indicating a >100-fold fluctuation of abundance between individual plants. Using restriction analysis of recA for a total of 285 confirmed isolates of the B. cepacia complex, up to seven B. cepacia complex species were identified; however, their diversity and abundance were not evenly distributed among individual plants, and several allelic variants were commonly found from the same rhizosphere sample. These results indicate that not only complex communities of B. cepacia complex species and closely related strains of the same species may coexist at high population levels but also species composition and abundance may dramatically vary between individual plants.     

Plant Functional Diversity and Species Diversity in the Mongolian Steppe

Background

The Mongolian steppe is one of the most important grasslands in the world but suffers from aridization and damage from anthropogenic activities. Understanding structure and function of this community is important for the ecological conservation, but has seldom been investigated.

Methodology/Principal Findings

In this study, a total of 324 quadrats located on the three main types of Mongolian steppes were surveyed. Early-season perennial forbs (37% of total importance value), late-season annual forbs (33%) and late-season perennial forbs (44%) were dominant in meadow, typical and desert steppes, respectively. Species richness, diversity and plant functional type (PFT) richness decreased from the meadow, via typical to desert steppes, but evenness increased; PFT diversity in the desert and meadow steppes was higher than that in typical steppe. However, above-ground net primary productivity (ANPP) was far lower in desert steppe than in the other two steppes. In addition, the slope of the relationship between species richness and PFT richness increased from the meadow, via typical to desert steppes. Similarly, with an increase in species diversity, PFT diversity increased more quickly in both the desert and typical steppes than that in meadow steppe. Random resampling suggested that this coordination was partly due to a sampling effect of diversity.

Conclusions/Significance

These results indicate that desert steppe should be strictly protected because of its limited functional redundancy, which its ecological functioning is sensitive to species loss. In contrast, despite high potential forage production shared by the meadow and typical steppes, management of these two types of steppes should be different: meadow steppe should be preserved due to its higher conservation value characterized by more species redundancy and higher spatial heterogeneity, while typical steppe could be utilized moderately because its dominant grass genus Stipa is resistant to herbivory and drought.     

Abundance and Diversity of Sulfate-Reducing Bacteria in High Arsenic Shallow Aquifers

The abundance, diversity, and relative distribution of sulfate-reducing bacteria (SRB) in high arsenic (As) groundwater aquifers of Hangjinhouqi County in the Hetao Basin, Inner Mongolia was investigated using denaturing gradient gel electrophoresis (DGGE) and quantitative polymerase chain reaction (qPCR) analysis of dsrB genes (encoding dissimilatory sulfite reductase beta-subunit). DGGE results revealed that SRB populations were diverse, but were mainly composed of Desulfotomaculum, Desulfobulbus, Desulfosarcina, and Desulfobacca. The abundance of Desulfobulbus was positively correlated with the ratio of Fe(II)/Fe(III). Although qPCR results showed that the dsrB gene abundance in groundwater samples ranged from below detection to 4.9 × 10⁶ copies/L, and the highest percentage of dsrB gene copies to bacterial 16S rRNA gene copies was 2.1%. Geochemical analyses showed that As(III) content and the ratio of Fe(II) to Fe(III) increased with total As, while sulfate concentrations decreased. Interestingly, the dsrB gene abundance was positively correlated with As concentrations. These results indicate that sulfate reduction occurs simultaneously with As and Fe reduction, and might result in increased As release and mobilization when As is not incorporated into iron sulfides. This study improves our understanding of SRB and As cycling in high As groundwater systems.     

Effects of Management Intensity and Season on Arboreal Ant Diversity and Abundance in Coffee Agroecosystems

Agricultural intensification decreases arthropod predator diversity, abundance and population stability, and may affect interactions between top predators and their arthropod prey – ultimately affecting ecosystem services. Coffee management intensification (reduction or removal of shade trees) reduces diversity of arthropod predators (ground-foraging ants). Because ants provide ecosystem services by controlling pests, influences of intensification on arboreal, coffee-foraging ant diversity and abundance are important. We here address how coffee intensification affects: (1) coffee-foraging ant diversity and abundance and (2) seasonal fluctuations in ant abundance. In each of four coffee sites of varying management intensity in Chiapas, Mexico, we sampled vegetation and using two methods, sampled ant diversity and abundance over two years. Sites significantly differed in vegetation and management intensity. Coffee-foraging ant diversity generally decreased with increasing management intensity (16–26% fewer species observed in the most intensively-managed site). Ant abundance was higher in the wet season. Management intensity, however, did not influence ant abundance or seasonal fluctuations in abundance. Our results highlight the importance of diverse agricultural systems in maintaining arthropod predator diversity, and point to one model system in which we may effectively test how diversity per se affects ecosystem services.     

Abundance and Diversity of Ammonia-Oxidizing Bacteria and Archaea in Cold Springs on the Qinghai-Tibet Plateau

The cold springs underlain by gas hydrates on the Qinghai-Tibet Plateau (QTP) are similar to deep-sea cold seeps with respect to methane biogeochemistry. Previous studies have shown that ammonia oxidizing bacteria (AOB) and archaea (AOA) are actively present and play important roles in the carbon/nitrogen cycles in cold seeps. Studying AOA and AOB communities in the QTP cold springs will be of great importance to our understanding of carbon and nitrogen cycling dynamics related to the underlying gas hydrates on the QTP. Thus, the abundance and diversity of AOB and AOA in sediments of four cold springs underlain by gas hydrates on the QTP were determined by using quantitative polymerase chain reaction and amoA gene (encoding ammonia monooxygenase involved in ammonia oxidation) phylogenetic analysis. The results showed that the AOB and AOA amoA gene abundances were at 10³–10⁴ copies per gram of the sediments in the investigated cold springs. The AOB population consisted of Nitrosospira and Nitrosomonas in contrast with the mere presence of Nitrosospira in marine cold seeps. The AOB diversity was higher in cold springs than in cold seeps. The AOA population was mainly composed of Nitrososphaera, in contrast with the dominance of Nitrosopumilus in cold seeps. The terrestrial origin and high level of dissolved oxygen of the cold springs may be the main factors accounting for the observed differences in AOB and AOA populations between the QTP cold springs and marine cold seeps.     

The Effect of Resource Islands on Abundance and Diversity of Bacteria in Arid Soils

Bacteria and nutrients were determined in upper soil samples collected underneath and between canopies of the dominant perennial in each of three sites along a steep precipitation gradient ranging from the Negev desert in the south of Israel to a Mediterranean forest in the north. Bacterial abundance, monitored by phospholipid fatty acid analysis, was significantly higher under the shrub canopy (compared to barren soils) in the arid and semi-arid sites but not in the Mediterranean soils. Bacterial community composition, determined using terminal restriction fragment length polymorphism and clone libraries, differed according to the sample’s origin. Closer examination revealed that in the arid and semi-arid sites, α-Proteobacteria are more abundant under the shrub canopy, while barren soils are characterized by a higher abundance of Actinobacteria. The bacterial communities in the Mediterranean soils were similar in both patch types. These results correspond to the hypothesis of “resource islands”, suggesting that shrub canopies provide a resource haven in low-resource landscapes. Yet, a survey of the physicochemical parameters of inter- and under-shrub soils could not attribute the changes in bacterial diversity to soil moisture, organic matter, or essential macronutrients. We suggest that in the nutrient-poor soils of the arid and semi-arid sites, bacteria occupying the soil under the shrub canopy may have longer growth periods under favorable conditions, resulting in their increased biomass and altered community composition.     

Diversity and Abundance of Ammonia-Oxidizing Archaea and Bacteria in Diverse Chinese Paddy Soils

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) in three types of paddy soils of China before and after rice plantation were investigated by using an integrated approach including geochemistry, 454 pyrosequencing, and quantitative polymerase chain reaction (PCR). The abundances of AOA amoA gene were 1～2 orders of magnitude higher than AOB amoA gene. The types of paddy soils had important impacts on the diversities of both AOA and AOB via clay mineralogy (smectite or illite-rich) and bioavailability of ammonium. The Nitrososphaera subcluster 5 and Nitrosopumilis cluster of AOA, and Nitrosomonas subcluster 5 and Nitrosospira subcluster 3 of AOB were well adapted to soils with high ammonium concentrations. AOA and AOB community structures were different before and after rice plantation, likely due to changes of pH and ammonium fertilization. The Nitrosospira subclusters 2 and 9 were well adapted to acidic paddy soils. However, the sensitivity of AOA and AOB community structures to these factors may be complicated by other geochemical conditions. The results of this study collectively demonstrated that multiple environmental factors, such as clay mineralogy, ammonium content and total organic carbon as well as soil pH, shaped AOA and AOB community structure and abundance.