Effects of organism size and community composition on ecosystem functioning

We tested (1) if the size of dominant species influenced ecosystem functioning in food webs consisting of bacteria, algae, and protozoa; (2) whether those effects changed in importance through time; and (3) how those effects compared with differences in diversity among experimental food webs. We constructed food webs using two size fractions of organisms that differed in individual mass by approximately two orders of magnitude. We measured total biomass and respiration (total CO₂ production) as two aspects of ecosystem functioning. We also compared these size‐dependent patterns in functioning across two levels of species richness. Initially, organism size strongly influenced total community biomass. With time, however, biomass and respiration eventually converged in communities dominated by large or small species. We conclude that after sufficient time for community development any differences in ecosystem functioning resulted from differences in community composition, including species richness, but not the size of the dominant organisms.     

Effects of naphthalene on microbial community composition in the Delaware estuary

The effects of naphthalene on microbial communities in the bottom boundary layer of the Delaware Bay estuary were investigated in microcosms using denaturing gradient gel electrophoresis (DGGE) and fluorescent in situ hybridization (FISH) with oligonucleotide probes. Three days after the addition of naphthalene, rates of bacterial production and naphthalene mineralization were higher than in no-addition controls and than in cases where glucose was added. Analyses using both DGGE and FISH indicated that the bacterial community changed in response to the addition of naphthalene. FISH data indicated that a few major phylogenetic groups increased in response to the glucose addition and especially to the naphthalene addition. DGGE also demonstrated differences in community composition among treatments, with four phylotypes being unique to naphthalene-amended treatments and three of these having 16S rRNA genes similar to known hydrocarbon degraders. The bacterial community in the naphthalene-amended treatment was distinct from the communities in the glucose-amended treatment and in the no-addition control. These data suggest that polycyclic aromatic hydrocarbons may have large effects on microbial community structure in estuaries and probably on microbially mediated biogeochemical processes.     

Earthworm effects without earthworms: inoculation of raw organic matter with worm-worked substrates alters microbial community functioning

Background

Earthworms are key organisms in organic matter decomposition because of the interactions they establish with soil microorganisms. They enhance decomposition rates through the joint action of direct effects (i.e. effects due to direct earthworm activity such as digestion, burrowing, etc) and indirect effects (i.e. effects derived from earthworm activities such as cast ageing). Here we test whether indirect earthworm effects affect microbial community functioning in the substrate, as when earthworms are present (i. e., direct effects).

Methodology/Principal Findings

To address these questions we inoculated fresh organic matter (pig manure) with worm-worked substrates (vermicompost) produced by three different earthworm species. Two doses of each vermicompost were used (2.5 and 10%). We hypothesized that the presence of worm-worked material in the fresh organic matter will result in an inoculum of different microorganisms and nutrients. This inoculum should interact with microbial communities in fresh organic matter, thus promoting modifications similar to those found when earthworms are present. Inoculation of worm-worked substrates provoked significant increases in microbial biomass and enzyme activities (β-glucosidase, cellulase, phosphatase and protease). These indirect effects were similar to, although lower than, those obtained in pig manure with earthworms (direct and indirect earthworm effects). In general, the effects were not dose-dependent, suggesting the existence of a threshold at which they were triggered.

Conclusion/Significance

Our data reveal that the relationships between earthworms and microorganisms are far from being understood, and suggest the existence of several positive feedbacks during earthworm activity as a result of the interactions between direct and indirect effects, since their combination produces stronger modifications to microbial biomass and enzyme activity.     

三种种植方式对土壤微生物群落组成的影响

土壤微生物是表征土壤质量变化的敏感指标之一。借助长期定位试验, 采用磷脂脂肪酸分析方法研究了3种种植方式(玉米(Zea mays)连作、玉米非连作和撂荒)对土壤微生物群落组成的影响。结果表明, 在不同的种植方式下, 土壤微生物群落组成有明显的差异。玉米连作的土壤中总磷脂脂肪酸和细菌磷脂脂肪酸含量最低, 分别为33.12 nmol·g^-1和18.09 nmol·g^-1。非连作的土壤真菌磷脂脂肪酸和真菌/细菌分别为0.61 nmol·g^-1和3.06%, 显著低于撂荒和连作(p < 0.05), 非连作方式下, 革兰氏阳性细菌/革兰氏阴性细菌增大。撂荒土壤的总磷脂脂肪酸和细菌磷脂脂肪酸分别为42.98和24.68 nmol·g^-1, 高于耕作处理。 同时, 在撂荒方式下, 革兰氏阳性细菌和革兰氏阴性细菌的含量增加, 革兰氏阳性细菌/革兰氏阴性细菌降低。主成分分析结果表明: 耕作处理(玉米连作和非连作)分布第一主成分负方向上, 第一主成分得分系数分别为-2.48和-1.84; 撂荒分布第一主成分正方向上, 第一主成分得分系数为2.31, 与连作和非连作差异显著(p < 0.05)。冗余分析(RDA)表明: 土壤pH、总氮、有效磷和土壤>0.25 mm水稳性团聚体含量与磷脂脂肪酸呈正相关, 并且土壤pH和土壤>0.25 mm水稳性团聚体含量对土壤微生物群落的影响最大。     

The effect of earthworms on the physiological state of the microbial community at vermicomposting

The effect of earthworms on the microbial community of composts and vermicomposts was assayed by the following parameters: mineralization activity, the levels of physiologically active and growing microbial biomass, the requirement for growth factors, and the spectrum of assimilation of organic substrates by the microbial community. The substrate affinities of microbial enzyme systems in vermicompost were found to be lower than in compost without earthworms, which is evidence of a higher amount of r-strategists in the microbial community of vermicomposts. Physiologically active biomass of microorganisms is higher in peat-based vermicompost than in compost. The microorganisms of vermicomposts and composts experience deficiency in growth factors to a lesser extent than the microorganisms in soil. The presence of earthworms influences the physiological diversity: the Shannon index increases or decreases depending on the type of composted substrate and incubation time. The growth rate of microorganisms increases on various test substrates in the presence of worms.     

微生物菌剂对猪粪堆肥中细菌群落结构的影响

以猪粪和小麦秸秆做堆肥试验,处理组添加外源微生物菌剂,利用常规方法对堆肥样品进行理化性状测定,采用高通量测序技术分析堆肥过程中细菌群落特征。理化性状测定结果表明: 添加外源菌剂可延长堆肥高温时间,降低堆肥发酵末期的pH,增加全氮含量,加快C/N的下降。主成分分析表明: 外源菌剂影响堆肥样品细菌群落的稳定性。门分类水平上,厚壁菌门、变形菌门和绿弯菌门的相对丰度在处理组中较高;纲分类水平上,梭状芽孢杆菌纲、α-变形菌纲和γ-变形菌纲在处理组的升温期和高温期相对丰度增加;科分类水平上,小单孢菌科和梭状芽孢杆菌纲的消化链球菌科、梭菌科以及盐厌氧菌科的相对丰度在处理组的升温期和高温期均呈上升趋势。Pearson相关性分析表明,盐胞菌属与外源菌剂呈显著正相关,而氨苄芽孢杆菌属与外源菌剂呈显著负相关。研究表明,猪粪堆肥中添加外源菌剂可使堆肥的理化性质和细菌群落结构均发生显著变化。     

The influence of soluble microbial products on microbial community composition: hypothesis of microbial community succession

Soluble microbial products (SMP) are organic compounds produced by activated sludge microorganisms as they degrade substrates. They include by-products of microbial activity, death and lysis. The available literature does not reveal how SMP influence microbial community composition. In this regard, we microscopically studied changes in composition of microbial communities, especially protozoa and metazoa, under the influence of increased as well as reduced levels of SMP. The presence of SMP at high level significantly caused changes in microbial community composition. Microbial species shifted from attached ciliates (12-175 microm) to free-swimming and crawling ciliates (35-330 microm) and then invertebrates, which included rotifers (0.2-1 mm) and nematodes (1-50 mm). The shift of small-size microorganisms to large ones was observed as one of the most significant influences of SMP. Attached ciliates reappeared when we removed the SMP that had accumulated in the bioreactors - we have called this as the resurrection phenomenon of microorganisms. Such rapid changes in microbial community composition were not observed in the experiment with low concentration of SMP. Overall, the results suggest that accumulation of SMP is one of the intrinsic regulatory mechanisms that control viability and dormancy of microbial communities in activated sludge.     

凋落物多样性及组成对凋落物分解和土壤微生物群落的影响

凋落物分解是生态系统营养物质循环的核心过程,而土壤微生物群落在凋落物分解过程中扮演着极其重要且不可替代的角色。随着生物多样性的丧失日益严峻,探讨凋落物多样性及组成对凋落物分解和土壤微生物群落的影响,不仅有助于了解凋落物分解的内在机制,而且可为退化草原生态系统的恢复提供参考。以内蒙古呼伦贝尔草原退化恢复群落中的草本植物为研究对象,依据植物多度、盖度、频度和物种的重要值及其在群落中的恢复程度筛选出排序前4的羊草（Leymus chinensis）、茵陈蒿（Artemisia capillaris）、麻花头（Serratula centauroides）、二裂委陵菜（Potentilla bifurca）的凋落物为实验材料,通过设置3种凋落物多样性水平（1,2,4）,包括11种凋落物组合（单物种凋落物共4种,两物种凋落物混合共6种,四物种凋落物混合共1种）,利用磷脂脂肪酸（PLFA）方法来研究分解60 d后凋落物多样性及组成对凋落物分解和土壤微生物群落的影响。结果表明：（1）凋落物物种多样性仅对C残余率具有显著影响,表现在两物种混合凋落物C残余率显著低于单物种凋落物,而凋落物组成对所观测的4个凋落物分解参数（质量、C、N残余率以及C/N）均具有显著影响;（2）凋落物物种多样性对细菌（B）含量具有显著影响,而凋落物组成对真菌（F）含量具有显著影响,两者对F/B以及微生物总量均无显著影响;（3）冗余分析结果表明凋落物组成与凋落物分解相关指标（凋落物质量、C、N残余率及C/N）和土壤微生物（真菌、细菌含量）的相关关系高于凋落物多样性。（4）进一步建立结构方程模型（Structural Equation Model,SEM）发现,凋落物初始C含量对凋落物质量、C、N残余率及C/N有显著正的直接影响;凋落物木质素含量对凋落物质量、C、N残余率有显著正的直接影响;凋落物初始N含量对N残余率有显著正的直接影响,而对C残余率及C/N有显著负的直接影响;凋落物初始C/N对凋落物质量、N残余率有显著正的直接影响,而对C/N有显著负的直接影响。此外,凋落物初始C、N、木质素含量及C/N均对真菌含量具有显著正影响,并可通过真菌对凋落物质量分解产生显著负的间接影响。以上结果表明该退化恢复区域优势种凋落物分解以初始C、木质素为主导,主要通过土壤真菌影响凋落物的分解进程,这将减缓凋落物的分解速率进而减慢草原生态系统的进程。这些结果为凋落物多样性及组成对自身分解和土壤微生物群落的影响提供了实验依据,也为进一步分析凋落物分解内在机制以及草原生态系统的恢复提供了数据参考。     

荒漠-绿洲土壤微生物群落组成与其活性对比

结合野外观测与实验室研究方法,对比研究了准葛尔盆地南缘盐生荒漠与绿洲农田土壤微生物活性与其群落组成的变化特征,并分析了土壤温度与湿度对荒漠-绿洲土壤微生物活性的影响。结果表明:荒漠开垦为绿洲后,土壤细菌明显增加,真菌无明显变化,放线菌显著减少。细菌在绿洲农田土壤矿化作用中占主导,真菌则在荒漠中占优势,绿洲农田土壤微生物活性(包括真菌与细菌活性)明显高于荒漠。温度对荒漠-绿洲土壤微生物活性的影响只在一定土壤湿度范围内作用显著,绿洲农田受其影响较大;荒漠有机质含量明显高于绿洲农田,但水分与盐分因素抑制了微生物对其的分解和矿化。不同土地利用方式导致了荒漠绿洲间土壤湿度及盐份的较大差异,加之与土壤温度极显著的交互作用,使得开垦后土壤有机碳的易得性增强,微生物群落结构发生显著改变,进而有机碳的矿化速率加快,土壤碳库随之消减。     

亚热带树种转换对林地土壤微生物群落结构和功能的影响

通过分析杉木采伐迹地营造阔叶树种尾巨桉和固氮树种黑木相思人工林后土壤微生物群落组成和酶活性,探讨造林树种转换对于改善杉木林地土壤微生物特性的影响.结果表明: 树种转换对土壤微生物群落组成和酶活性的影响主要局限于0～10 cm土壤层.杉木转换为固氮树种黑木相思后,显著提高了0～10 cm土壤层总脂肪酸含量、真菌、革兰氏阳性细菌、革兰氏阴性细菌和放线菌生物量.主成分分析表明,黑木相思人工林土壤微生物群落组成与杉木和尾巨桉人工林具有显著差异,土壤中革兰氏阳性细菌、阴性细菌和放线菌丰度显著提高.在0～10 cm土壤层,黑木相思人工林土壤纤维素水解酶、乙酰氨基-葡萄糖苷酶和酸性磷酸酶活性均显著高于杉木和尾巨桉人工林.研究表明,杉木转变为固氮树种黑木相思后会显著提高微生物生物量和酶活性,有助于土壤有机质的恢复,加快养分循环过程.     

林下植物剔除对毛竹林土壤微生物群落结构的影响

本研究以中亚热带地区广泛分布的毛竹林为对象,采用随机区组实验设计,分析了林下植物剔除对毛竹林土壤微生物群落结构和土壤理化特性的影响,探讨林下植物对毛竹林土壤微生物群落结构的调控机制.结果 表明:林下植物剔除对土壤理化特性产生显著影响,主要表现为土壤全氮、硝态氮和有效磷含量增加,而土壤铵态氮、全磷含量及土壤pH值降低.此...     

Influence of soil pollution on the composition of a microbial community

The abundance dynamics and composition of indigenous soil microbial communities were studied in soils polluted with naphthalene, dioctyl phthalate, diesel fuel, and crude oil. DGGE analysis of the 16S rRNA genes amplified from the total soil DNA revealed that the bacterial community of uncontaminated soil was more diverse and included no dominant species. In the soil samples polluted with the crude oil, diesel fuel, or dioctyl phthalate, Pseudomonas became the dominant bacteria since the third day of the experiment. In the soil polluted with naphthalene, two genera of bacteria (Pseudomonas and Paenibacillus) were dominant in population on the third day of the experiment, while on the 21th day of the experiment Arthrobacter became dominant. During the experiment, the average number of indigenous bacterial degraders increased approximately by two orders of magnitude. While the key genes of naphthalene catabolism, nahAc and nahH, were not detected in the pristine soil, they were found in a significant amount on the third day after naphthalene addition. Three degrader strains harboring the plasmids of naphthalene biodegradation (IncP-9 group) were isolated on the third day from the soil polluted with naphthalene. Two of these plasmids, although isolated from various degraders, were shown to be identical.     

The importance of dispersal for bacterial community composition and functioning

We conducted a metacommunity experiment to investigate the role of dispersal for bacterial community composition (BCC) and function of freshwater bacteria. Bacteria were dispersed from a common source pool into three different lake communities in their natural lake water. The experiment was conducted in dialysis bags to enable a decoupling between a change in the local environment and dispersal. BCC was determined by terminal restriction fragment length polymorphism (tRFLP) of the 16S rRNA gene. We show that the greatest changes in BCC occurred between 10% and 43% of dispersal of standing stock per day. Functioning, measured as growth rate, was also affected by dispersal in all three communities but the qualitative pattern differed between communities, sometimes showing a hump-shaped relationship to dispersal and sometimes decreasing with increasing dispersal. In all waters, functioning was related to BCC. Our results show that dispersal does affect BCC and functioning but that high dispersal rates are needed. Further, the effect of dispersal on BCC and function seem to depend on the quality of the habitat to which bacteria disperse into.     

Changes in microbial biomass,community composition and diversity,and functioning with soil depth in two alpine ecosystems on the Tibetan plateau

Plant and Soil - Plant P acquisition strategies are driven by multiple belowground morphological and physiological traits as well as interactions among these traits. This study aimed to...     

Unraveling negative biotic interactions determining soil microbial community assembly and functioning

Microbial communities play important roles in all ecosystems and yet a comprehensive understanding of the ecological processes governing the assembly of these communities is missing. To address the role of biotic interactions between microorganisms in assembly and for functioning of the soil microbiota, we used a top-down manipulation approach based on the removal of various populations in a natural soil microbial community. We hypothesized that removal of certain microbial groups will strongly affect the relative fitness of many others, therefore unraveling the contribution of biotic interactions in shaping the soil microbiome. Here we show that 39% of the dominant bacterial taxa across treatments were subjected to competitive interactions during soil recolonization, highlighting the importance of biotic interactions in the assembly of microbial communities in soil. Moreover, our approach allowed the identification of microbial community assembly rule as exemplified by the competitive exclusion between members of Bacillales and Proteobacteriales. Modified biotic interactions resulted in greater changes in activities related to N- than to C-cycling. Our approach can provide a new and promising avenue to study microbial interactions in complex ecosystems as well as the links between microbial community composition and ecosystem function.Subject terms: Soil microbiology, Ecology     

Silicon-rich soil amendments impact microbial community composition and the composition of arsM bearing microbes

Plant and Soil - Arsenic (As) cycling in flooded rice paddies is driven by soil microbes which among other transformations can cause conversion between inorganic and organic As species. Silicon...     

Exploring mixed microbial community functioning: recent advances in metaproteomics

System approaches to elucidate ecosystem functioning constitute an emerging area of research within microbial ecology. Such approaches aim at investigating all levels of biological information (DNA, RNA, proteins and metabolites) to capture the functional interactions occurring in a given ecosystem and track down characteristics that could not be accessed by the study of isolated components. In this context, the study of the proteins collectively expressed by all the microorganisms present within an ecosystem (metaproteomics) is not only crucial but can also provide insights into microbial functionality. Overall, the success of metaproteomics is closely linked to metagenomics, and with the exponential increase in the availability of metagenome sequences, this field of research is starting to experience generation of an overwhelming amount of data, which requires systematic analysis. Metaproteomics has been employed in very diverse environments, and this review discusses the recent advances achieved in the context of human biology, soil, marine and freshwater environments as well as natural and bioengineered systems.     

Effects of understory removal on soil respiration and microbial community composition structure in a Chinese fir plantation

Aims Soil respiration (R_s) is the largest fraction of carbon flux in forest ecosystems, but the effects of forest understory removal on R_s in Chinese fir (Cunninghamia lanceolate) plantations is poorly understood. In order to quantify the effects of forest understory removal on R_s and microbial community composition, a field experiment was conducted in a subtropical Chinese fir plantation. Methods Forest understory was removed manually in June 2012. R_s was measured monthly using a LI-COR 8100 infrared gas analyzer from July 2012 through July 2014. Soil temperature and moisture were also measured at 5 cm depth at the time of R_s measurements. Surface soil (0-10 cm) samples were collected in July 2013 and 2014, respectively, and the soil microbial community structures were determined by phospholipid fatty acids (PLFAs) analysis. Important findings R_s decreased by 32.8% over a two-year period following understory removal (UR), with a greater rate of decrease in the first year (42.9%) than in the second year (22.2%). The temperature sensitivity of R_s was affected by UR, and was 2.10 and 1.87 in the control and UR plots, respectively. UR significantly reduced the concentration of fungal PLFAs by 18.3%, but did not affect the concentration of bacterial PLFAs, resulting in an increase in the fungal:bacterial ratio; it significantly increased the concentration of gram-positive bacterial PLFAs by 24.5%, and the ratio of gram-positive to gram-negative bacterial PLFAs after one year of treatment, but decreased the concentration of gram-positive bacterial PLFAs by 9.4% and the ratio of gram-positive to gram-negative bacterial PLFAs after two years of treatment. The results suggested that R_s and microbial community composition were both affected by UR in Chinese fir plantation, and the effects were dependent of the duration following the UR treatment.