Alteration of microbial community composition and changes in decomposition associated with an invasive intertidal macrophyte

Data demonstrating the effects of biological invaders on microbial communities and microbial processes are scarce, especially in marine environments. Research was conducted at Padilla Bay, Washington, to examine the effect that an invasive intertidal eelgrass, Zostera japonica Aschers & Graebn, has on rates of decomposition, microbial community composition, and the possible implications for associated ecosystem processes in this estuarine environment. A series of observational and experimental studies were conducted in beds of Z. japonica, beds of its native congener, Zostera marina, and mixed eelgrass beds. These studies assessed decomposition of invasive and native eelgrass, enumerated bacterial abundance, and examined sole source carbon usage (SSCU) by microbial assemblages. Z. japonica decomposed more rapidly than its native congener throughout the study period although rates of decomposition were variable. Microbial abundance did not differ among different vegetation compositions although differences in SSCU by microbial assemblages were detected among beds of invasive, native, and mixed eelgrass. These results indicate that this abundant invasive species can accelerate rates of decomposition and alter the associative decomposer community, which may lead to higher carbon and nutrient turnover within Padilla Bay.     

The influence of the invasive shrub, Lonicera maackii, on leaf decomposition and microbial community dynamics

Amur honeysuckle (Lonicera maackii) is an exotic invasive shrub that is rapidly expanding into forests of eastern North America. This species forms a dense forest understory, alters tree regeneration, negatively affects herb-layer biodiversity, and alters ecosystem function. In a second-growth forest in central Kentucky, we examined the timing and production of leaf litter and compared litter chemistry, decay rates, and microbial community colonization of Amur honeysuckle to that of two native trees, white ash (Fraxinus americana) and hickory (Carya spp.). The distribution of Amur honeysuckle was clumped, allowing us to compare differences in decomposition under and away from Amur honeysuckle shrubs. Amur honeysuckle leaf litter had significantly higher nitrogen, lower C:N, and lower lignin than the other species, and decomposition rates were greater than 5×?faster. Despite the much higher rate of Amur honeysuckle decomposition compared with the native species (p?<?0.0001), decomposition of all species was significantly slower (p?=?0.0489) in sites located under Amur honeysuckle shrubs. Nitrogen concentration increased through time in decomposing Amur honeysuckle litter; however, total mass of N rapidly declined. We found the initial microbial community on leaf litter of Amur honeysuckle was distinct from two native species and although all microbial communities changed through time, the microbial community of Amur honeysuckle remained distinct from native communities. In summary, a distinct microbial community that may originate on Amur honeysuckle leaves prior to senescence could explain the rapid decay rates.     

Interactions between an arbuscular mycorrhizal fungus and a soil microbial community mediating litter decomposition

We investigated arbuscular mycorrhizal fungi (AMF) alteration of microbial mediation of litter decomposition. AMF (Glomus hoi) were either allowed access to or excluded from Plantago lanceolata L. root litter embedded in soil; litter was labeled with either (13) C only or (13) C and (15) N. Plant N uptake was significantly increased if AMF accessed the litter, and (15) N analysis of the plant material indicated that 2-3% of plant N originated from litter. Succession of the soil community mediating decomposition was assessed by phospholipid fatty acids (PLFA) combined with (13) C-PLFA. During the first 21?days of decomposition, saprotrophic fungi and Gram-negative bacteria were the dominant consumers of litter C. As decomposition progressed however, (13) C content of the fungal biomarkers declined substantially, and Gram-negative and Gram-positive bacteria became the primary reservoirs of labeled litter C. The putative PLFA marker for AMF (16:1ω5c) originated primarily from non-AMF sources. In AMF-invaded root litter, Gram-negative, Gram-positive, and 16:1ω5c markers became less (13) C-enriched relative to their counterparts in non-AMF-invaded microcosms during active decomposition. These patterns of (13) C: (12) C enrichment may result from AMF supply of (12) C from the plant to the decomposing soil microbial community; such C inputs could alter the microbial mediation of litter decomposition.     

植被对土壤微生物群落结构的影响

研究了不同土壤及覆盖其上的植被与土壤微生物群落结构和多样性的关系．植被使土壤中的微生物种类更丰富,群落多样性更高．表层土壤微生物群落中没有明显的优势种群,种间竞争作用较弱．并介绍了研究土壤微生物群落的分子生物学方法．     

Cover thresholds for impacts of an exotic grass on the structure and assembly of a wet prairie community

Potential impacts of an exotic grass, Hemarthria altissima, on restoration of wet prairie community structure (species richness and cover of indicator species) and assembly processes (temporal turnover rates of plant species) on the Kissimmee River floodplain in Central Florida, USA, were evaluated over a 12-year period before and after restoration of hydrologic regimes (2001), and implementation of herbicide treatments (2006–2007) to control its spread. Thresholds for impacts were derived from comparisons of sample sites with variable levels of H. altissima cover. Prior to herbicide treatments, cover of H. altissima exhibited a logistic increase over time, with peak colonization and expansion occurring during major flood events. Mean post-restoration cover of three native wet prairie indicator species (Polygonum punctatum, Panicum hemitomon, and Luziola fluitans) increased to 37.8 ± 3.4 % in plots in which H. altissima cover was <12 %, and did not exceed 15 % in any plots with H. altissima cover >30 %. Prior to and after herbicide treatments, these indicator species largely accounted for observed differences in wet prairie community structure (i.e., cover of wetland forbs and grasses) between heavily infested sites and plots with low or no cover of H. altissima. The cover threshold at which H. altissima began to have these community-level effects was 40–50 %, but lower species richness was found only where H. altissima cover was >80 %. Increasing cover of H. altissima led to a significant decline in temporal turnover rates of plant species (P < 0.001, r² = 0.10), but also was largely due to plots with very high (>75 %) cover of H. altissima. Mean temporal turnover rates of plant species increased significantly (P = 0.03) after herbicide treatments and subsequently were highest during an ensuing flood pulse. However, 2–3 years after herbicide treatments, regrowth of H. altissima reestablished high cover (mean = 59 ± 9.5 %) in over half of the treated plots. The ability of H. altissima to establish dominant cover in restored hydrologic conditions on the Kissimmee River floodplain, and documented regrowth following herbicide treatments, increase the potential for this exotic grass species to be a pervasive threat to successful reestablishment of wet prairie community structure and assembly processes.     

Labile soil carbon inputs mediate the soil microbial community composition and plant residue decomposition rates

Root carbon (C) inputs may regulate decomposition rates in soil, and in this study we ask: how do labile C inputs regulate decomposition of plant residues, and soil microbial communities? In a 14 d laboratory incubation, we added C compounds often found in root exudates in seven different concentrations (0, 0.7, 1.4, 3.6, 7.2, 14.4 and 21.7 mg C g(-1) soil) to soils amended with and without (13) C-labeled plant residue. We measured CO(2) respiration and shifts in relative fungal and bacterial rRNA gene copy numbers using quantitative polymerase chain reaction (qPCR). Increased labile C input enhanced total C respiration, but only addition of C at low concentrations (0.7 mg C g(-1)) stimulated plant residue decomposition (+2%). Intermediate concentrations (1.4, 3.6 mg C g(-1)) had no impact on plant residue decomposition, while greater concentrations of C (>7.2 mg C g(-1)) reduced decomposition (-50%). Concurrently, high exudate concentrations (>3.6 mg C g(-1)) increased fungal and bacterial gene copy numbers, whereas low exudate concentrations (<3.6 mg C g(-1)) increased metabolic activity rather than gene copy numbers. These results underscore that labile soil C inputs can regulate decomposition of more recalcitrant soil C by controlling the activity and relative abundance of fungi and bacteria.     

Refuge effect of an unpalatable forb on community structure and grass morphology in a temperate grassland

The role of unpalatable plant species as biological antiherbivore refuges for palatable species is well-documented at community level particularly in harsh environments. In productive sub-humid temperate grassland subjected to domestic grazing, we examined the protective effect of Eryngium horridum on plant community structure and floristic composition, and evaluated whether these changes impacted on a number of morphological traits of grasses, related to grazing resistance. We also investigated, for a palatable grass species (Stipa neesiana) the existence of morphological differences between protected and unprotected plants and if this eventual variation was either plastic or genetic. The study consisted of a field survey where we compared paired patches, with and without E. horridum, and a greenhouse experiment where we evaluated individuals of S. neesiana coming from both patch types over a 11 months period. Patches dominated by E. horridum had lower richness and cover of forbs than patches without the forb, and similar richness but greater cover of cool-season tussock palatable grasses, which suggests a protective role on the latter. Grasses in these patches also had longer blades and sheaths and lower specific leaf area. The morphological differences of S. neesiana individuals collected from both patch types disappeared after 11 months growth in a common environment which revealed significant phenotypic plasticity in this species. These results suggest the existence of plant-to-plant facilitation in a productive ecosystem not only at community level, through changes in species richness and the promotion of palatable grasses, but also at population level, through plastic changes in aboveground morphological traits. Both facilitation and plasticity, would contribute to the persistence of threatened palatable grasses in the heavy grazed productive ecosystems.     

Effect of dissolved organic carbon quality on microbial decomposition and nitrification rates in stream sediments

1. Microbial decomposition of dissolved organic carbon (DOC) contributes to overall stream metabolism and can influence many processes in the nitrogen cycle, including nitrification. Little is known, however, about the relative decomposition rates of different DOC sources and their subsequent effect on nitrification. 2. In this study, labile fraction and overall microbial decomposition of DOC were measured for leaf leachates from 18 temperate forest tree species. Between 61 and 82% (mean, 75%) of the DOC was metabolized in 24 days. Significant differences among leachates were found for labile fraction rates (P < 0.0001) but not for overall rates (P=0.088). 3. Nitrification rates in stream sediments were determined after addition of 10 mg C L^–1 of each leachate. Nitrification rates ranged from below detection to 0.49 μg N mL sediment^–1 day^–1 and were significantly correlated with two independent measures of leachate DOC quality, overall microbial decomposition rate (r=–0.594, P=0.0093) and specific ultraviolet absorbance (r=0.469, P=0.0497). Both correlations suggest that nitrification rates were lower in the presence of higher quality carbon. 4. Nitrification rates in sediments also were measured after additions of four leachates and glucose at three carbon concentrations (10, 30, and 50 mg C L^–1). For all carbon sources, nitrification rates decreased as carbon concentration increased. Glucose and white pine leachate most strongly depressed nitrification. Glucose likely increased the metabolism of heterotrophic bacteria, which then out‐competed nitrifying bacteria for NH₄⁺. White pine leachate probably increased heterotrophic metabolism and directly inhibited nitrification by allelopathy.     

Priority effects: How the order of arrival of an invasive grass,Bromus tectorum,alters productivity and plant community structure when grown with native grass species

Theories and models attempt to explain how and why particular plant species grow together at particular sites or why invasive exotic species dominate plant communities. As local climates change and human‐use degrades and disturbs ecosystems, a better understanding of how plant communities assemble is pertinent, particularly when restoring grassland ecosystems that are frequently disturbed. One such community assembly theory is priority effects, which suggests that arrival order of species into a community alters plant–plant interactions and community assembly. Theoretically, priority effects can have lasting effects on ecosystems and will likely be altered as the risk of invasion by exotic species increases. It is difficult to predict how and when priority effects occur, as experimental reconstruction of arrival order is often difficult in adequate detail. As a result, limited experimental studies have explored priority effects on plant community assembly and plant invasions. To determine if and how priority effects affect the success of invasive species, we conducted a greenhouse study exploring how the arrival order of an invasive grass, Bromus tectorum, affects productivity and community composition when grown with native grasses. We found evidence for priority effects, as productivity was positively related to dominance of B. tectorum and was greater the earlier B. tectorum arrived. This suggests that priority effects could be important for plant communities as the early arrival of an invasive species drastically impacted the productivity and biodiversity of our system at the early establishment stages of plant community development.     

Effect of pyocyanin on a crude-oil-degrading microbial community

Pseudomonas aeruginosa is an n-alkane degrader that is frequently isolated from petroleum-contaminated sites and produces factors that enhance its competitiveness and survival in many environments. In this study, one such factor, pyocyanin, has been detected in an oil-degrading culture containing P. aeruginosa and is a redox-active compound capable of inhibiting microbial growth. To examine the effects of pyocyanin further, an oil-degrading culture was grown with and without 9.5 microM pyocyanin and microbial community structure and oil degradation were monitored for 50 days. Denaturing gradient gel electrophoresis (DGGE) analysis of cultures revealed a decrease in the microbial community diversity in the pyocyanin-amended cultures compared to that of the unamended cultures. Two members of the microbial community in pure culture exhibited intermediate and high sensitivities to pyocyanin corresponding to intermediate and low levels of activity for the antioxidant enzymes catalase and superoxide dismutase, respectively. Another member of the community that remained constant in the DGGE gels over the 50-day culture incubation period exhibited no sensitivity to pyocyanin, corresponding to a high level of catalase and superoxide dismutase when examined in pure culture. Pyocyanin also affected the overall degradation of the crude oil. At 50 days, the culture without pyocyanin had decreased polycyclic aromatic hydrocarbons compared to the pyocyanin-amended culture, with a specific reduction in the degradation of dibenzothiophenes, naphthalenes, and C(29) and C(30) hopanes. This study demonstrated that pyocyanin influenced the diversity of the microbial community and suggests the importance of understanding how interspecies interactions influence the degradation capability of a microbial community.     

培养条件下二氯喹啉酸对土壤微生物群落结构的影响

为探讨除草剂二氯喹啉酸对土壤微生物群落结构的影响,在25℃黑暗培养条件下,采用磷脂脂肪酸法(Phospholipid Fatty Acid,PLFA)分析了二氯喹啉酸(0对照、83.3和166.6μg/kg干土)处理对淹水和不淹水水田土壤微生物群落结构的影响。结果表明,在实验处理的60 d内,不淹水水田土壤在83.3μg/kg二氯喹啉酸处理后对土壤微生物生物总量、细菌生物量及真菌生物量有抑制作用,而166.6μg/kg二氯喹啉酸处理后各生物量指标均显著增加,但是两种浓度处理均使土壤真菌/细菌比值下降,说明二氯喹啉酸处理会使不淹水水田土壤微生物稳定性下降;淹水水田土壤在83.3μg/kg二氯喹啉酸处理下,对土壤微生物生物总量和真菌生物量有促进作用,对细菌生物量有一定的抑制作用,166.6μg/kg二氯喹啉酸处理对土壤微生物生物总量、细菌及真菌生物量均有促进作用,从真菌/细菌比值上看,不同浓度处理与对照无显著差异,说明二氯喹啉酸对淹水生物稳定性无明显干扰。PLFA主成分分析表明,不同浓度处理的两种土壤微生物群落均以含14∶0、15∶0、16∶0和18∶2n6c的微生物为优势种群。     

Nitrogenase gene diversity and microbial community structure: a cross-system comparison

Biological nitrogen fixation is an important source of fixed nitrogen for the biosphere. Microorganisms catalyse biological nitrogen fixation with the enzyme nitrogenase, which has been highly conserved through evolution. Cloning and sequencing of one of the nitrogenase structural genes, nifH, has provided a large, rapidly expanding database of sequences from diverse terrestrial and aquatic environments. Comparison of nifH phylogenies to ribosomal RNA phylogenies from cultivated microorganisms shows little conclusive evidence of lateral gene transfer. Sequence diversity far outstrips representation by cultivated representatives. The phylogeny of nitrogenase includes branches that represent phylotypic groupings based on ribosomal RNA phylogeny, but also includes paralogous clades including the alternative, non-molybdenum, non-vanadium containing nitrogenases. Only a few alternative or archaeal nitrogenase sequences have as yet been obtained from the environment. Extensive analysis of the distribution of nifH phylotypes among habitats indicates that there are characteristic patterns of nitrogen fixing microorganisms in termite guts, sediment and soil environments, estuaries and salt marshes, and oligotrophic oceans. The distribution of nitrogen-fixing microorganisms, although not entirely dictated by the nitrogen availability in the environment, is non-random and can be predicted on the basis of habitat characteristics. The ability to assay for gene expression and investigate genome arrangements provides the promise of new tools for interrogating natural populations of diazotrophs. The broad analysis of nitrogenase genes provides a basis for developing molecular assays and bioinformatics approaches for the study of nitrogen fixation in the environment.     

钾肥及与秸秆配施对紫色土作物产量和微生物群落结构的影响

基于紫色菜园土壤莴笋-白菜-甜玉米轮作4年12季连续定位施钾肥试验,研究不同种类钾肥及用量对重庆地区紫色菜园土上作物产量和土壤微生物群落结构的影响,为该地区作物生产确定合理的施钾技术提供科学依据。结果表明,在施用氮磷肥基础上,不同钾肥处理莴笋、白菜、甜玉米产量均显著提高;从3种作物4年平均产量和钾肥效益看,以单施适量化学钾(K_2)、单施适量秸秆钾(M_2)和秸秆还田配施少量化学钾(K_1+M_1)的施钾肥模式对白菜的增产效果好,增产28.05%—30.27%;M_2和K_1+M_1施钾肥模式对莴笋的增产效果较好,增产13.89%和13.81%;K_1+M_1施钾肥模式对甜玉米的增产效果最好,增产15.10%,表明秸秆还田配施少量化学钾(K_1+M_1)模式在供试3种作物生产中具有很好的应用前景。不同施钾处理对土壤微生物群落结构及丰度均会产生一定影响,以秸秆还田配施少量化学钾肥(K_1+M_1)对提高土壤细菌、真菌、革兰氏阳性菌的作用较好,并显著增加土壤微生物总PLFA含量,缓解对土壤微生物生存环境的胁迫,说明K_1+M_1能为土壤微生物的生长繁育创造有利环境。莴笋、白菜、甜玉米3种作物4年平均产量与土壤细菌、真菌、革兰氏阳性菌和革兰氏阴性菌数量间存在显著相关性(P0.05),而不同钾肥处理对土壤微生物特征具有一定影响,说明施钾肥可能会调节土壤微生物特征,从而促进作物增产。     

模拟增温及分解界面对茭草凋落物分解速率及叶际微生物结构和功能的影响

挺水植物的凋落物是湿地生态系统物质循环的重要组成部分, 阐明气候变暖以及生境差异对湿地挺水植物凋落物分解过程及叶际微生物的影响对揭示湿地生态系统关键物质循环过程具有重要意义。该研究以滇西北高原典型湿地优势挺水植物茭草(Zizania latifolia)为研究对象, 采用凋落物袋法研究了茭草在模拟增温(1.5-2.0 ℃)及不同生境(大气界面、水界面与土界面)下的质量残留率和叶际微生物数量、结构组成与功能代谢特征。研究发现: 模拟气候变暖及生境差异均显著影响凋落物的分解速率。经过一年的分解, 凋落物在模拟增温环境下的质量残留率为66.4%, 对照组的质量残留率为77.7%, 增温组分解常数(k)值是对照组的1.64倍, 而凋落物在水界面与土界面的质量残留率为42.2%和25.3%, 其k值分别为大气界面的3.63和5.25倍, 生境差异是影响湿地挺水植物凋落物分解速率的关键因素。模拟增温主要改变了凋落物叶际微生物的群落组成特征, 而生境变化主要影响叶际微生物的绝对数量、微生物多样性、群落结构组成以及功能代谢活性。处于土界面的凋落物叶际微生物具有最高的群落功能代谢活性及醇类碳源利用程度。不同处理之间的植物叶际微生物特征与凋落物分解速率具有较好的一致性, 为揭示湿地植物凋落物分解快慢的微生物驱动机制提供了重要的理论依据。     

Litter quality versus soil microbial community controls over decomposition: a quantitative analysis

The possible effects of soil microbial community structure on organic matter decomposition rates have been widely acknowledged, but are poorly understood. Understanding these relationships is complicated by the fact that microbial community structure and function are likely to both affect and be affected by organic matter quality and chemistry, thus it is difficult to draw mechanistic conclusions from field studies. We conducted a reciprocal soil inoculum × litter transplant laboratory incubation experiment using samples collected from a set of sites that have similar climate and plant species composition but vary significantly in bacterial community structure and litter quality. The results showed that litter quality explained the majority of variation in decomposition rates under controlled laboratory conditions: over the course of the 162-day incubation, litter quality explained nearly two-thirds (64 %) of variation in decomposition rates, and a smaller proportion (25 %) was explained by variation in the inoculum type. In addition, the relative importance of inoculum type on soil respiration increased over the course of the experiment, and was significantly higher in microcosms with lower litter quality relative to those with higher quality litter. We also used molecular phylogenetics to examine the relationships between bacterial community composition and soil respiration in samples through time. Pyrosequencing revealed that bacterial community composition explained 32 % of the variation in respiration rates. However, equal portions (i.e., 16 %) of the variation in bacterial community composition were explained by inoculum type and litter quality, reflecting the importance of both the meta-community and the environment in bacterial assembly. Taken together, these results indicate that the effects of changing microbial community composition on decomposition are likely to be smaller than the potential effects of climate change and/or litter quality changes in response to increasing atmospheric CO₂ concentrations or atmospheric nutrient deposition.     

Soil and plant effects on microbial community structure

We investigated the effects of two different plant species (corn and soybean) and three different soil types on microbial community structure in the rhizosphere. Our working hypothesis was that the rhizosphere effect would be strongest on fast-growing aerobic heterotrophs, while there would be little or no rhizosphere effect on oligotrophic and other slow-growing microorganisms. Culturable bacteria and fungi had larger population densities in the rhizosphere than in bulk soil. Communities were characterized by soil fatty acid analysis and by substrate utilization assays for bacteria and fungi. Fatty acid analysis revealed a very strong soil effect but little plant effect on the microbial community, indicating that the overall microbial community structure was not affected by the rhizosphere. There was a strong rhizosphere effect detected by the substrate utilization assay for fast-growing aerobic heterotrophic bacterial community structure, with soil controls and rhizosphere samples clearly distinguished from each other. There was a much weaker rhizosphere effect on fungal communities than on bacterial communities as measured by the substrate utilization assays. At this coarse level of community analysis, the rhizosphere microbial community was impacted most by soil effects, and the rhizosphere only affected a small portion of the total bacteria.     

Rat invasion of islands alters fungal community structure,but not wood decomposition rates

Introduced animals can indirectly affect decomposers through trophic cascades and habitat modifications, but whether their effects are strong enough to influence both the structure and function of decomposer communities remains unclear. We conducted an experiment on rat‐invaded and rat‐free islands off the coast of New Zealand to determine whether introduced rats affected the structure and function of wood‐decomposing fungi. Gamma‐irradiated branch segments from a single tree were placed on the forest floor on nine rat‐invaded and nine rat‐free islands, and fungal community structure and wood decomposition rates measured after two years of in situ decomposition. We found significant differences in fungal community structure in the wood between rat‐invaded and rat‐free islands. Furthermore, there was a significant correlation between fungal community structure and wood decomposition rate on rat‐free islands but not on rat‐invaded islands, because of decreased variability in decomposition rates on invaded islands. Despite these differences between rat‐free and rat‐invaded islands, mean decomposition rates were indistinguishable between the two sets of islands. These results suggest that there may be a great deal of functional redundancy in fungal communities and that removing rats from islands could reverse the rat‐induced changes that we observed in the relationship between the structure and function of decomposer communities.     

Habitat structure modified by an invasive grass enhances inundation withstanding in a salt-marsh wolf spider

Vegetation and underground structures are known to influence flood avoidance and flood resistance in invertebrates. In bimonthly-flooded European salt marshes, recent invasions by the nitrophilous grass Elymus athericus strongly modified usual habitat structure, notably by the production of a deep litter layer. Consequently, invaded habitats provide more interstitial spaces that may act as a refuge during flood events. By using both controlled and field designs, we tested whether invaded habitats may change the ability to resist flooding by the creation of new refuges during tides for a ground-living, predatory arthropod. The wolf spider Arctosa fulvolineata was employed as a model species since it occurs abundantly in both invaded and uninvaded salt-marsh habitats. In the field, its abundance strongly decreased (divided by three) after tidal flooding in uninvaded habitats by but did not change in invaded patches. Under controlled laboratory conditions, ten times more individuals withstood simulated flooding in the presence of litter and less decided to float. The presence of litter did not influence flood resistance, i.e. survival underwater. Our results show that habitat structure (i.e. the presence of litter) influences flood-avoiding behavior of A. fulvolineata, by providing more refuges. As the invasion of E. athericus alters salt-marsh habitat structure, it may enhance population size of a rare predatory spider by changing its behavior during flooding and resulting in less deleterious impacts of tides. Yet biological invasions are detrimental for biodiversity conservation, our study shows that an invasive species might indirectly benefit a few mobile rare species in a flood-disturbed habitat.