Comparison of Soil Bacterial Communities Under Diverse Agricultural Land Management and Crop Production Practices

The composition and structure of bacterial communities were examined in soil subjected to a range of diverse agricultural land management and crop production practices. Length heterogeneity polymerase chain reaction (LH-PCR) of bacterial DNA extracted from soil was used to generate amplicon profiles that were analyzed with univariate and multivariate statistical methods. Five land management programs were initiated in July 2000: conventional, organic, continuous removal of vegetation (disk fallow), undisturbed (weed fallow), and bahiagrass pasture (Paspalum notatum var Argentine). Similar levels in the diversity of bacterial 16S rDNA amplicons were detected in soil samples collected from organically and conventionally managed plots 3 and 4 years after initiation of land management programs, whereas significantly lower levels of diversity were observed in samples collected from bahiagrass pasture. Differences in diversity were attributed to effects on how the relative abundance of individual amplicons were distributed (evenness) and not on the total numbers of bacterial 16S rDNA amplicons detected (richness). Similar levels of diversity were detected among all land management programs in soil samples collected after successive years of tomato (Lycopersicon esculentum) cultivation. A different trend was observed after a multivariate examination of the similarities in genetic composition among soil bacterial communities. After 3 years of land management, similarities in genetic composition of soil bacterial communities were observed in plots where disturbance was minimized (bahiagrass and weed fallow). The genetic compositions in plots managed organically were similar to each other and distinct from bacterial communities in other land management programs. After successive years of tomato cultivation and damage from two major hurricanes, only the composition of soil bacterial communities within organically managed plots continued to maintain a high degree of similarity to each other and remain distinct from other bacterial communities. This study reveals the effects of agricultural land management practices on soil bacterial community composition and diversity in a large-scale, long-term replicated study where the effect of soil type on community attributes was removed.     

Change within and among forest communities: the influence of historic disturbance,environmental gradients,and community attributes

Understanding how ecological communities change over time is critical for biodiversity conservation, but few long‐term studies directly address decadal‐scale changes in both the within‐ and among‐community components of diversity. In this study, we use a network of permanent forest vegetation plots, established in Great Smoky Mountains National Park (USA) in 1978, to examine the factors that influence change in community composition within and among communities. In 2007, we resampled 15 plots that were logged in the late 1920s and 15 plots that had no documented history of intensive human disturbance. We found that understory species richness decreased by an average of 4.3 species over the 30‐yr study period in the logged plots, but remained relatively unchanged in the unlogged plots. In addition, tree density decreased by an average of 145 stems ha^?1 in the logged plots, but was relatively stable in the unlogged plots. However, we found that historic logging had no effect on within‐community understory or tree compositional turnover during this time period. Instead, sites at lower elevations and sites with lower understory biomass in 1978 had higher understory compositional turnover than did sites at higher elevations and sites with higher understory biomass. In addition, sites with lower soil cation exchange capacity (CEC) and with lower tree basal area in 1978 had higher tree compositional turnover than did sites with higher soil CEC and higher tree basal area. Among‐community similarity was unchanged from 1978 to 2007 for both the logged and unlogged plots. Overall, our results indicate that human disturbance can affect plant communities for decades, but the extent of temporal change in community composition may nevertheless depend more on environmental gradients and community attributes.     

茂县土地岭植被恢复过程中物种多样性动态特征

植被恢复是退化生态系统重建的重要途径,植被恢复过程物种多样性的变化反映了植被的恢复程度.通过群落调查和多样性分析,研究了岷江上游土地岭植被恢复过程中群落物种多样性特征.结果表明： 恢复过程中6类不同类型群落分别表现其对于不同环境特征、干扰及更新方式等的响应;森林是较灌丛更适合当地环境状况的植被类型;人工恢复无干扰和轻度干扰群落的多样性相对较高,是较好的恢复模式.重度干扰使得1年生植物与地下芽植物比例增加,其它口食性较好的多年生草本减少.较强的干扰是群落无法更新、长期处于灌丛阶段且多样性较低的重要原因.本地区人工恢复群落在更新进程和多样性维持上优于自然更新群落,种植华山松加速了本地区植被演替进程.建议以适合恢复区域的多种恢复配置方式进行造林,并避免较强干扰,可以加速群落演替进程并保持恢复群落较高的物种丰富度与多样性.     

Community Turnover of Wood-Inhabiting Fungi across Hierarchical Spatial Scales

For efficient use of conservation resources it is important to determine how species diversity changes across spatial scales. In many poorly known species groups little is known about at which spatial scales the conservation efforts should be focused. Here we examined how the community turnover of wood-inhabiting fungi is realised at three hierarchical levels, and how much of community variation is explained by variation in resource composition and spatial proximity. The hierarchical study design consisted of management type (fixed factor), forest site (random factor, nested within management type) and study plots (randomly placed plots within each study site). To examine how species richness varied across the three hierarchical scales, randomized species accumulation curves and additive partitioning of species richness were applied. To analyse variation in wood-inhabiting species and dead wood composition at each scale, linear and Permanova modelling approaches were used. Wood-inhabiting fungal communities were dominated by rare and infrequent species. The similarity of fungal communities was higher within sites and within management categories than among sites or between the two management categories, and it decreased with increasing distance among the sampling plots and with decreasing similarity of dead wood resources. However, only a small part of community variation could be explained by these factors. The species present in managed forests were in a large extent a subset of those species present in natural forests. Our results suggest that in particular the protection of rare species requires a large total area. As managed forests have only little additional value complementing the diversity of natural forests, the conservation of natural forests is the key to ecologically effective conservation. As the dissimilarity of fungal communities increases with distance, the conserved natural forest sites should be broadly distributed in space, yet the individual conserved areas should be large enough to ensure local persistence.     

Effects of selective logging on tree species diversity and composition of Bornean tropical rain forests at different spatial scales

Reduced-impact logging (RIL) is known to be beneficial in biodiversity conservation, but its effects on tree diversity remain unknown. Pattern of tree diversity following disturbance usually varies with spatial scale of sampling (i.e., plot size). We examined the impacts of RIL on species richness and community composition of tree species at different spatial scales, and the scale (plot size) dependency of the two metrics; species richness versus community similarity. One 2-ha and three to four 0.2-ha plots were established in each of primary, RIL, and conventionally logged (CL) forest in Sabah, Malaysia. Species richness (the number of species per unit number of stems) was higher in the RIL than in the CL forest at both scales. The relationship between species richness and logging intensity varied with plot size. Species richness was greater in the RIL than in the primary forest at the 2-ha scale, while it was similar between the two forests at 0.2-ha scale. Similarly, species richness in the CL forest demonstrated a greater value at the 2-ha scale than at the 0.2-ha scale. Greater species richness in the two logged forests at the 2-ha scale is attributable to a greater probability of encountering the species-rich, small patches that are distributed heterogeneously. Community composition of the RIL forest more resembled that of the primary forest than that of the CL forest, regardless of plot size. Accordingly, species richness is a scale-dependent metric, while community similarity is a more robust metric to indicate the response of tree assemblage to anthropogenic disturbance.     

The impact of natural resource use on bird and reptile communities within multiple-use protected areas: evidence from sub-arid Southern Madagascar

Multiple-use protected areas, in which sustainable levels of extractive livelihood activities are permitted, play an increasingly important role in the global protected area estate, and are expected to rise in prevalence. However, we know little about their effectiveness at conserving biodiversity. We surveyed bird and reptile communities in three areas across a forest disturbance gradient resulting from charcoal production and shifting cultivation within a multiple-use protected area in Madagascar’s sub-arid spiny forest. We scored individual species using a Conservation Value Index (CVI; a simple metric based on rarity, threat and distinctiveness), and estimated the total conservation value of each treatment by calculating the sum of frequency-weighted CVI scores across all present species. Bird and reptile community responses to forest disturbance were idiosyncratic. Bird richness was greatest in the moderate-disturbance treatment, but the low-disturbance treatment had the superior conservation value due to higher frequencies of locally-endemic species. Reptile richness was the same in low- and moderate-disturbance treatments, but the conservation value of the latter was greater. The high-disturbance areas had lowest richness and conservation value for both groups. For birds, increasing disturbance levels were accompanied by community turnover from high-value to low-value species, a pattern highlighted by CVI that is masked by assessing species richness alone. Although some endemic species appear to be resilient to degradation, multiple-use protected areas in Madagascar may lose biodiversity since most endemic species are forest-dependent. Stricter protected area models may be more appropriate in areas where much of the high-value biodiversity is sensitive to habitat degradation.     

Methods matter: Different biodiversity survey methodologies identify contrasting biodiversity patterns in a human modified rainforest — A case study with amphibians

Understanding how well tropical forest biodiversity can recover following habitat change is often difficult due to conflicting assessments arising from different studies. One often overlooked potentially confounding factor that may influence assessments of biodiversity response to habitat change, is the possibility that different survey methodologies, targeting the same indicator taxon, may identify different patterns and so lead to different conclusions. Here we investigated whether two different but commonly used survey methodologies used to assess amphibian communities, pitfall trapping and nocturnal transects, indicate the same or different responses of amphibian biodiversity to historic human induced habitat change. We did so in a regenerating rainforest study site located in one of the world’s most biodiverse and important conservation areas: the Manu Biosphere Reserve. We show that the two survey methodologies tested identified contrasting biodiversity patterns in a human modified rainforest. Nocturnal transect surveys indicated biodiversity differences between forest with different human disturbance histories, whereas pitfall trap surveys suggested no differences between forest disturbance types, except for community composition. This pattern was true for species richness, diversity, overall abundance and community evenness and structure. For some fine scale metrics, such as species specific responses and abundances of family groups, both methods detected differences between disturbance types. However, the direction of differences was inconsistent between methods. We highlight that for assessments of rainforest recovery following disturbance, survey methods do matter and that different biodiversity survey methods can identify contrasting patterns in response to different types of historic disturbance. Our results contribute to a growing body of evidence that arboreal species might be more sensitive indicators than terrestrial communities.     

Patterns in woody species diversity, richness and partitioning of diversity in forest communities of tropical deciduous forest biome

The regressive succession model hypothesizes tropical savanna-woodlands to be a degraded stage of primary deciduous forests. Species diversity, richness and evenness of woody species in savanna-woodlands, secondary deciduous forests and mature deciduous forests of central India were compared to test if the regressive succession explained pattern in species richness, diversity, functional diversity and basal area. At the plot scale (0.1 ha) secondary deciduous forests and savanna-woodlands had similar species diversity, a pattern not consistent with the regressive model of deciduous forest succession, and mature deciduous forests had greater species diversity and richness (p<0.05). When examined at a larger scale or community scale by pooling all plots within a community type, the trend in diversity persisted even with greater effort allocated to sampling of secondary deciduous forests. Species richness at the community scale was greatest in secondary deciduous forest as expected from species area relationship. The communities shared 28 woody species but the species composition was significantly different between the communities. I suggest that conservation of tropical deciduous forests based on regressive succession model is problematic.     

Plant community ecology of Pinus sylvestris, an extirpated species reintroduced to Ireland

Plantation forests can make a significant contribution to the conservation of native biodiversity, especially where native forest cover is low. Ireland is used as a case study to explore the contribution to biodiversity made by stands of Pinus sylvestris (Scots pine), a reintroduced species. Despite its disputed native status, P. sylvestris is being widely planted in semi-natural habitats in Ireland. The associated vegetation communities have not previously been described and their conservation value is unknown. Baseline information is needed to inform conservation and forest management strategies. Botanical surveys were carried out at 20 plots of P. sylvestris-dominated woodland and scrub throughout the Republic of Ireland. Vegetation, structural and environmental data were recorded. Data were analysed using non-parametric and multivariate statistical techniques and a synoptic table was prepared. P. sylvestris was found to be a non-specialist in terms of its environmental tolerances. β diversity among plots was high while α diversity within plots was low to moderate. The plots surveyed contained 14.2% of the Irish native flora. There was a low level of constancy of species. Four reasonably well defined vegetation communities were identified. Soil pH, altitude and slope had important roles in partitioning these vegetation types and soil pH was positively correlated with species richness. P. sylvestris is well established, well integrated and naturalising in Irish semi-natural habitats. Some of the associated vegetation communities corresponded to habitats of international conservation importance. This research demonstrates that stands of P. sylvestris represent an important resource for Ireland’s native botanical and habitat diversity.     

Past Human Disturbance Effects upon Biodiversity are Greatest in the Canopy; A Case Study on Rainforest Butterflies

A key part of tropical forest spatial complexity is the vertical stratification of biodiversity, with widely differing communities found in higher rainforest strata compared to terrestrial levels. Despite this, our understanding of how human disturbance may differentially affect biodiversity across vertical strata of tropical forests has been slow to develop. For the first time, how the patterns of current biodiversity vary between three vertical strata within a single forest, subject to three different types of historic anthropogenic disturbance, was directly assessed. In total, 229 species of butterfly were detected, with a total of 5219 individual records. Butterfly species richness, species diversity, abundance and community evenness differed markedly between vertical strata. We show for the first time, for any group of rainforest biodiversity, that different vertical strata within the same rainforest, responded differently in areas with different historic human disturbance. Differences were most notable within the canopy. Regenerating forest following complete clearance had 47% lower canopy species richness than regenerating forest that was once selectively logged, while the reduction in the mid-storey was 33% and at ground level, 30%. These results also show for the first time that even long term regeneration (over the course of 30 years) may be insufficient to erase differences in biodiversity linked to different types of human disturbance. We argue, along with other studies, that ignoring the potential for more pronounced effects of disturbance on canopy fauna, could lead to the underestimation of the effects of habitat disturbance on biodiversity, and thus the overestimation of the conservation value of regenerating forests more generally.     

四川盆周低山暴雨区不同配置模式水土保持林生物多样性分析

用物种多样性指数(Shannon-Wienner指数、Simpson指数)、均匀度指数(Pielou)和物种丰富度指数(Margalef指数和Menhinick指数)对广元市7种人工森林群落进行多样性分析。结果表明,植被恢复与重建使生物多样性提高的同时,土壤侵蚀模数比治理前下降了45%;乔、灌、草复层经营对生物多样性与水土保持效益具有同样的贡献;水土保持效益因不同森林群落的生物多样性而异。     

Importance of semi-natural habitats for the conservation of butterfly communities in landscapes dominated by pine plantations

While the area of plantation forests continues to increase worldwide, their contribution to the conservation of biodiversity is still controversial. There is a particular concern on the central role played by natural habitat remnants embedded within the plantation matrix in conserving species-rich insect communities. We surveyed butterflies in maritime pine plantation landscapes in south-western France in 83 plots belonging to seven habitat types (five successional stages of pine stands, native deciduous woodlands and herbaceous firebreaks). The effect of plot, habitat and landscape attributes on butterfly species richness, community composition and individual species were analysed with a General Linear Model (GLM), partial Canonical Correspondence Analysis (CCA) and the IndVal method. The most important factors determining butterfly diversity and community composition were the presence of semi-natural habitats (deciduous woodlands and firebreaks) at the landscape scale and the composition of understorey vegetation at the plot scale. Pure effects of plot variables explained the largest part of community variation (12.8%), but landscape factors explained an additional, independent part (6.7%). Firebreaks were characterized by a higher species richness and both firebreaks and deciduous woodlands harboured species not or rarely found in pine stands. Despite the forest-dominated landscape, typical forest butterflies were rare and mainly found in the deciduous woodlands. Threatened species, such as Coenonympha oedippus and Euphydryas aurinia, were found in pine stands and in firebreaks, but were more abundant in the latter. In the studied plantation forest, the conservation of butterflies depends mainly on the preservation of semi-natural habitats, an adequate understorey management and the maintenance of soil moisture levels.     

Local-scale spatial diversity patterns of ectomycorrhizal fungal communities in a subtropical pine-oak forest

This study aimed to analyze spatial patterns of soil ectomycorrhizal fungal (EMF) communities at the local scale in a subtropical pine-oak forest located in the Nearctic-Neotropical transition in central Mexico, to underpin biodiversity conservation strategies in forest fragments of this region. We used a spatially-explicit nested square sampling design with the same sampling representativeness at all scales and replicated three times. We detected 674 EMF OTUs within 19,200 m² and 65 OTUs on average per sample. Seventy percent of OTUs were detected in only 1–4 samples. Average community similarity was below 5%, showed minor change within 14 and 339 m distance and increased with the spatial grain used to compare the data. We found a high species-area relationship and beta diversity coefficients for soil fungi indicating that, at the local scale, increasing area by a constant factor of four represented an increase in OTU richness by a factor of two.     

不同干扰强度下江西武夷山河岸带阔叶林群落的结构与数量特征

为揭示中亚热带典型河岸带阔叶林群落的结构特征、数量特征和干扰强度的耦合关系,根据干扰强度的不同,在江西武夷山保护区内选取3条主要水系进行阔叶林群落调查,共统计到河岸带维管束植物93科174属304种,分别占保护区维管束植物总数的41.5%、18.0%、11.9%。物种组成以壳斗科（6属22种）、山茶科（7属22种）、樟科（6属16种）、蔷薇科（8属16种）为主。不同干扰强度下的河岸带植被群落相似性Jaccard系数均在0.2-0.3之间,各群落优势种完全不同,且存在特有分布的物种,但群落乔木层优势种优势度（重要值）差异不显著（P〉0.05）。不同干扰强度下,物种数量、群落Jaccard系数、丰富度指数、多样性指数、均匀度指数总体上为：轻微干扰〉中等干扰〉无干扰;而乔木的平均高度和平均胸径却为：无干扰〉中等干扰〉轻微干扰。研究结果表明,江西武夷山河岸带阔叶林以常绿阔叶树种为主,但不同干扰梯度下群落的结构和数量特征差异性较大。     

浙江大雷山夏蜡梅群落植物物种多样性及其与土壤因子相关性

分别采用物种丰富度、物种多样性指数和群落均匀度等指标对浙江省大雷山夏蜡梅群落植物物种多样性进行测定,并通过相关分析对各种指数与土壤因子的关系进行研究。据10个样地统计,共有维管植物74科、165属、193种。从种子植物属的地理成分来看,温带分布的类型居多。不同群落木本植物的物种丰富度和多样性指数以杉木+木荷林最高,群落均匀度以杉木林最高,毛竹林的各项指数最低。草本植物的物种丰富度以杉木+马尾松林最高,杉木林最低;多样性指数和群落均匀度以竹林最高,短柄枹+格药柃林最低。在不同群落的垂直结构中,乔木层的物种丰富度和多样性指数均小于灌木层,草本层的物种多样性在不同群落间变化较大。相关分析表明,夏蜡梅群落物种多样性与土壤有机质含量相关性较大,其中,木本植物物种多样性与有机质含量显著正相关,草本植物与有机质含量显著负相关。     

水淹干扰下水库水滨带植物群落谱系结构与物种多样性格局

群落谱系结构将物种系统发育信息整合到群落中，给生物多样性研究提供了全新视角。为探讨水淹干扰下水库水滨带植物群落物种多样性维持机制，以丹江口水库水滨带为研究区域，以南水北调中线一期工程运行前的原有水滨带植被为研究对象，分析不同水淹干扰强度下群落谱系结构和物种多样性及其与环境因素的关系。结果表明：(1)随着水淹干扰强度增加，群落物种丰富度、物种多样性和谱系多样性显著降低。谱系结构指数虽无显著差异，但随着水淹干扰强度增加呈现由发散到聚集的变化趋势。表明水滨带植物群落物种多样性维持机制是生境过滤和生态位分化共同驱动的结果，并且随着水淹干扰强度增加呈现生境过滤作用增加、物种间竞争排斥作用减弱的生态过程影响规律。(2)坡度、土壤质地、速效氮和全氮含量对整个水滨带植物群落物种丰富度、物种多样性和谱系多样性影响显著。此外，土层厚度和速效磷对物种丰富度和土层厚度对谱系多样性也影响显著。而仅有速效氮含量对谱系结构指数影响显著；轻度水淹干扰下坡向、速效磷含量与多样性指数显著相关；中度水淹干扰下坡度、土层厚度、土壤质地、土壤总氮含量与多样性指数显著相关，土壤pH、全氮和全磷含量与谱系结构指数显著相关；重度水淹...     

美洲森林群落beta多样性的纬度梯度性

Beta多样性度量不同时空尺度物种组成的变化,是生物多样性的重要组成部分;理解其地理格局和形成机制已成为当前生物多样性研究的热点问题。基于Alwyn H. Gentry在美洲收集的131个森林样方数据,采用倍性和加性分配方法度量群落beta多样性,检验beta多样性随纬度的变化趋势,并分析其形成机制。研究表明:(1) 美洲森林群落beta多样性随纬度增加显著下降,热带和亚热带地区beta多样性高于温带地区;此格局可由物种分布范围的纬度梯度性和不同粒度(grain)下物种丰富度与纬度回归斜率的差异推论得出;(2) 加性分配方法表明beta多样性对各个温度带森林群落gamma多样性的相对贡献率平均为78.2%,并且随纬度升高而降低;(3) 美洲南半球森林群落beta多样性高于其北半球,这可能反映了区域间物种进化和环境变迁历史的差异。此外,还探讨了不同beta多样性计算方法的适用情景,首次证实了森林生态系统群落水平beta多样性的纬度梯度性,这对研究生物多样性的形成机制和生物多样性保护都具有重要的意义。     

大兴安岭森林火烧后不同演替阶段土壤细菌多样性动态

【目的】研究我国最大的林区之一——大兴安岭森林火烧后不同演替阶段土壤细菌多样性动态,为天然林保护工程对于生物多样性的影响增添新的认识。【方法】以空间替代时间的方法分析大兴安岭森林演替对于土壤细菌多样性动态的影响。大兴安岭森林火烧后典型的自然演替序列为火烧迹地(LG-BA)、灌丛(SHR)、白桦林(BP)、白桦落叶松混交林(BP-LG)、落叶松林(LG-OM)。在演替序列的每个典型样地上采集0-10 cm土样,采用Illumina Mi Seq高通量测序技术测定土壤细菌群落组成及其多样性。【结果】细菌操作分类单位(OTU)数量从少到多的顺序为火烧迹地落叶松白桦混交林灌丛落叶松林白桦林。随着森林演替,多样性指数Simpson先增高后降低;Shannon指数先增加后减少再增加;OTU的丰度变化比较平缓,表明物种变化较小。在各演替阶段中,土壤细菌种类主要有变形菌门(Proteobacteria)、酸杆菌门(Acidobacteria)、放线菌门(Actinobacteria)和浮霉菌门(Planctomycetes),4个门的种类含量随演替顺序都呈现先增加后减少的趋势。主成分分析表明不同演替阶段土壤细菌群落存在一定的差异性。冗余分析表明有机质(SOM)、全氮(TN)、全磷(TP)和p H对于土壤细菌群落变化有影响。【结论】随着森林演替,大兴安岭地区土壤细菌种类和生物多样性会发生变化,其变化与土壤化学成分和p H有关。