It has recently been proposed that many communities are structured by a hierarchy of interactions in which facilitation by foundation species is of primary importance. We conducted the first explicit experimental test of this hypothesis by investigating the organization of positive interactions on New England cobblestone beaches. In this midintertidal community, wave-generated substrate instability and solar stress largely limit marine organisms to the shelter of cordgrass beds. Cordgrass, which can establish and persist without the aid of other foundation species, facilitates a dense assemblage of inhabitants (e.g., mussels, snails, seaweeds) with roots/rhizomes that stabilize substrate and a dense canopy that baffles waves and provides shade. Within the cordgrass bed community, ribbed mussels further enhance physical conditions and densities of other species (e.g., amphipods, barnacles) by providing crevice space and hard substrate. We conclude that cordgrass bed communities are hierarchically organized: secondary interactions (e.g., facilitation by ribbed mussels) play a key role within an assemblage dependent on primary facilitation by the independently successful foundation species cordgrass. Our results identify emergent indirect positive interactions in the form of facilitation cascades, have broad implications for conservation, and help unify existing models of community organization that were developed without considering the fundamental role of positive interactions.

Metabarcoding potentially offers a rapid and cheap method of monitoring biodiversity, but real-world applications are few. We investigated its utility in studying patterns of litter arthropod diversity and composition in the tropics. We collected litter arthropods from 35 matched forest-plantation sites across Xishuangbanna, southwestern China. A new primer combination and the MiSeq platform were used to amplify and sequence a wide variety of litter arthropods using simulated and real-world communities. Quality filtered reads were clustered into 3,624 MOTUs at >= 97% similarity and the taxonomy of each MOTU was predicted. We compared diversity and compositional differences between forests and plantations (rubber and tea) for all MOTUs and for eight arthropod groups. We obtained similar to 100% detection rate after in silico sequencing six mock communities with known arthropod composition. Ordination showed that rubber, tea and forest communities formed distinct clusters. a-diversity declined significantly between forests and adjacent plantations for more arthropod groups in rubber than tea, and diversity of order Orthoptera increased significantly in tea. Turnover was higher in forests than plantations, but patterns differed among groups. Metabarcoding is useful for quantifying diversity patterns of arthropods under different land-uses and the MiSeq platform is effective for arthropod metabarcoding in the tropics.

To understand the influence of land use change on earthworm communities, the quantitative distribution of earthworms and its relationships with environmental factors in the tropical secondary forest and rubber plantation in Xishuangbanna, Southwest China were studied in January 2006. The results showed that after the secondary forest converted into rubber plantation, soil nutrients and organic C input from plants reduced significantly, and earthworm communities altered. In rubber plantation, the density of tropical exotic earthworm (<EM>Pontoscolex corethrurus</EM>) (52.27 ind·m<SUP>-2</SUP>) was significantly higher than that of native earthworm (<EM>Amynthas</EM> sp.) (0.53 ind·m<SUP>-2</SUP>); while in secondary forest, no significant differences were observed in the density and biomass of the two earthworm species. The density (0.53 ind·m<SUP>-2</SUP>) and biomass (0.32 g·m<SUP>-2</SUP>) of <EM>Amynthas</EM> sp. in rubber plantation showed a decrease trend compared with those in secondary forest (6.93 ind·m<SUP>-2</SUP>, 7.76 g·m<SUP>-2</SUP>). An increasing population of <EM>P. corethrurus</EM> was accounted by the larger proportion of its juvenile’s density and biomass, while <EM>Amynthas</EM> sp. was mainly composed of adults. The fine-root biomass of rubber plantation was positively correlated with the density of <EM>P. corethrurus</EM>. It was suggested that the vegetation change and soil nutrient decrease due to the conversion of secondary forest into rubber plantation had promoted the reproduction of exotic earthworm, and the adaptive strategies of exotic and native earthworms could not be ignored.

In this paper, the soil biodiversity and its functioning in ecosystem were briefly summarized, and the history and development of the discipline of soil biology were also reviewed. Meanwhile, I pointed out some issues on soil biology to be addressed for a few years to come. Due to the importance of soil biodiversity to the maintenance of ecosystem functions but inadequate study on soil biota in China, a series of articles on soil biota were collectively published in this issue of <em>Biodiversity Science</em>. The objectives of this issue were to enable the Chinese scientists to better understand the functions of soil biodiversity and to stimulate the interest of young scholars in the discipline of soil biology. The ultimate goal was to push forward the research and development of soil biology in China and to apply the knowledge and techniques of soil biology in the development of national economy.

本文概括性地介绍了土壤生物类群的多样性及其在生态系统中的作用; 同时简要地回顾和比较了国内外在土壤生物学方面的研究动态, 分析了土壤生物学今后的发展趋势。鉴于土壤生物在生态系统中的重要性以及我国在土壤生物学研究方面的不足, 《生物多样性》本期刊登了一系列有关土壤生物的文章, 目的是为了使国内科学家对土壤生物多样性在生态系统中的作用有更好的认识, 并希望能够唤起更多的年轻学者加入到土壤生物学研究的行列, 以推动土壤生物学在我国的迅速发展并将土壤生物学的研究成果应用于国民经济的发展中。

Insights into what stabilizes natural food webs have always been limited by a fundamental dilemma: Studies either need to make unwarranted simplifying assumptions, which undermines their relevance, or only examine few replicates of small food webs, which hampers the robustness of findings. We used generalized modeling to study several billion replicates of food webs with nonlinear interactions and up to 50 species. In this way, first we show that higher variability in link strengths stabilizes food webs only when webs are relatively small, whereas larger webs are instead destabilized. Second, we reveal a new power law describing how food-web stability scales with the number of species and their connectance. Third, we report two universal rules: Food-web stability is enhanced when (i) species at a high trophic level feed on multiple prey species and (ii) species at an intermediate trophic level are fed upon by multiple predator species.

Soil abiotic and biotic factors play key roles in plant community dynamics. However, little is known about how soil biota influence vegetation changes over time. Here, we show that the effects of soil organisms may depend on both the successional development of ecosystems and on the successional position of the plants involved. In model systems of plants and soils from different successional stages, we observed negative plant-soil feedback for early-successional plant species, neutral feedback for mid-successional species, and positive feedback for late-successional species. The negative feedback of early-successional plants was independent of soil origin, while late-successional plants performed best in late- and worst in early-successional soil. Increased performance of the subordinate, late-successional plants resulted in enhanced plant community diversity. Observed feedback effects were more related to soil biota than to abiotic conditions. Our results show that temporal variations in plant-soil interactions profoundly contribute to plant community assemblage and ecosystem development.

Large areas of rainforest in Asia have been converted to plantations, with uncertain effects on soil biodiversity. Using standard metagenetic methods, we compared the soil biota of bacteria, fungi, and nematodes at three rainforest sites in Malaysia with two rubber plantation sites with similar soils and geology. We predicted the following: (1) that the rubber sites would have a lower α- and β-diversity than the rainforest sites, due to the monospecific canopy cover and intensive management with herbicides, pesticides, and fertilizers, and (2) that due to differences in the physical and biotic environment associated with cultivation, there would be distinct communities of bacteria, fungi, and nematodes. However, regarding (1), the results showed no consistent difference in α- and β-diversity of bacteria, fungi, or nematodes between rainforest and rubber plantation sites. It appears that conversion of rainforest to rubber plantations does not necessarily result in a decrease in diversity of soil biota. It may be that heterogeneity associated with the cultivation regimen compensates for loss of biotically imposed heterogeneity of the original rainforest. Regarding (2), as predicted there were statistically significant differences in community composition between rainforest and rubber plantation for bacteria, fungi, and nematodes. These differences could be related to a range of factors including light level, litter fall composition, pH, C and N, selecting a distinct set of soil taxa, and it is possible that this in itself would affect long-term soil function.

In this study, we investigated the termite community in natural forests (tropical rain forest and evergreen broadleaved forest) and rubber plantation in Nabanhe Natural Reserve in Xishuangbanna, and explored the effects of rubber plantation on termite community structure, feeding group composition and diversity. The results are as follows: (1) A total of 397 samples of termites were collected in the three forest types, and 20 species of termites were identified belonging to 2 families and 10 genera. The dominant species were tropical termites; (2) Season was an important factor affecting the termite community, and the diversity of termites in the rainy season was higher than that in dry season; (3) The abundance, richness and diversity index of termites in the natural forests were significantly higher than that of rubber plantation. For feeding groups, the proportion of soilwood feeding termites in the rubber plantation was significantly lower than that in the natural forests, while the proportion of wood feeding termites in the rubber plantation was higher. Our results suggested that large areas of monocluture rubber plantations in tropical region have negative impacts on termite community structure and diversity. We recommend that polyculture rubber plantations as the alternative monoculture rubber plantations should be developed to protect termite diversity.

采用样带法对西双版纳纳板河自然保护区自然林(热带雨林和常绿阔叶林)和橡胶林白蚁群落进行了调查，探讨了橡胶林种植对白蚁群落结构、食性类群组成和多样性的影响。结果表明： (1)在3种森林类型中，共收集白蚁样本397份，隶属于2科10属20种，热带性白蚁种属组成突出；(2)季节对白蚁群落多度和丰富度有显著影响，总体表现为雨季高于旱季；(3)自然林中白蚁多度、丰富度和多样性指数显著高于单一橡胶林，且橡胶林中白蚁稀有种数量显著减少，同时土木食性白蚁的数量比例显著低于自然林，而木食性白蚁比例增加。研究认为，热带地区大面积单一橡胶林种植可对&ldquo;生态系统工程师&rdquo;白蚁群落结构和多样性产生较大的负面影响，应重视发展复合橡胶林模式保护白蚁生物多样性。

The conversion of monoculture rubber (Hevea brasiliensis) plantations into rubber-based agroforestry systems has become a common trend in forestry management in the past few decades. Rubber–Flemingia macrophylla (a leguminous shrub) systems are popular in southwestern China’s Xishuangbanna region. The biogeochemical cycles of soil carbon and nitrogen in forests are mainly affected by their fractions. This study investigated the effect of introducing Flemingia macrophylla to rubber plantations of different ages on soil carbon and nitrogen fractions. The experimental treatments included R1 (young rubber plantation), RF1 (young rubber–Flemingia macrophylla system), R2 (mature rubber plantation) and RF2 (mature rubber–Flemingia macrophylla system). The results showed that the introduction of Flemingia macrophylla to rubber plantations of different ages significantly changed soil carbon and nitrogen fractions, improved soil labile organic carbon and nitrogen contents, and ameliorated soil environments. The average soil microbial biomass organic carbon, nitrogen and nitrate-nitrogen in the 0–10 cm soil layer during the experimental period was 38.9%, 55.5%, and 214.7% higher in RF1 than R1, respectively, and 22.1%, 22.2%, and 652.2% higher in RF2 than R2, respectively. Therefore, Flemingia macrophylla can be used as an alternative interplanted tree species within rubber plantations in similar environments of southeastern Asia.

Freshwater salinization may result in significant changes of microbial community composition and diversity, with implications for ecosystem processes and function. Earlier research has revealed the importance of large shifts in salinity on microbial physiology and ecology, whereas studies on the effects of smaller or narrower shifts in salinity on the microeukaryotic community in inland waters are scarce. Our aim was to unveil community assembly mechanisms and the stability of microeukaryotic plankton networks at low shifts in salinity.Here, we analyzed a high-resolution time series of plankton data from an urban reservoir in subtropical China over 13 consecutive months following one periodic salinity change ranging from 0 to 6.1‰. We found that (1) salinity increase altered the community composition and led to a significant decrease of plankton diversity, (2) salinity change influenced microeukaryotic plankton community assembly primarily by regulating the deterministic-stochastic balance, with deterministic processes becoming more important with increased salinity, and (3) core plankton subnetwork robustness was higher at low-salinity levels, while the satellite subnetworks had greater robustness at the medium-/high-salinity levels. Our results suggest that the influence of salinity, rather than successional time, is an important driving force for shaping microeukaryotic plankton community dynamics.Our findings demonstrate that at low salinities, even small increases in salinity are sufficient to exert a selective pressure to reduce the microeukaryotic plankton diversity and alter community assembly mechanism and network stability. Our results provide new insights into plankton ecology of inland urban waters and the impacts of salinity change in the assembly of microbiotas and network architecture. Video abstract.

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning in terrestrial ecosystems. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. Here we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake. In mid-and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass or shift in bacterial-to-fungal ratio. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and/or fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered.

The composition of nematode communities (plant-parasitic and free-living) may be used as bioindicators of soil health or condition because composition correlates well with nitrogen cycling and decomposition, two critical ecological processes in soil. Maturity and trophic diversity indices withstand statistical rigor better than do abundances, proportions, or ratios of trophic groups. Maturity indices respond to a variety of land-management practices, based largely on inferred life history characteristics of families. Similarity indices may be more useful than diversity indices because they reflect taxon composition. Improving existing indices or developing alternative indices refined by a greater understanding of the biology of key taxa may enhance the utility of nematodes as bioindicators.

Nematodes play an important role in ecosystem processes, yet the relevance of nematode species diversity to ecology is unknown. Because nematode identification of all individuals at the species level using standard techniques is difficult and time-consuming, nematode communities are not resolved down to the species level, leaving ecological analysis ambiguous. We assessed the suitability of massively parallel sequencing for analysis of nematode diversity from metagenomic samples. We set up four artificial metagenomic samples involving 41 diverse reference nematodes in known abundances. Two samples came from pooling polymerase chain reaction products amplified from single nematode species. Two additional metagenomic samples consisted of amplified products of DNA extracted from pooled nematode species. Amplified products involved two rapidly evolving ~400-bp sections coding for the small and large subunit of rRNA. The total number of reads ranged from 4159 to 14771 per metagenomic sample. Of these, 82% were > 199 bp in length. Among the reads > 199 bp, 86% matched the referenced species with less than three nucleotide differences from a reference sequence. Although neither rDNA section recovered all nematode species, the use of both loci improved the detection level of nematode species from 90 to 97%. Overall, results support the suitability of massively parallel sequencing for identification of nematodes. In contrast, the frequency of reads representing individual species did not correlate with the number of individuals in the metagenomic samples, suggesting that further methodological work is necessary before it will be justified for inferring the relative abundances of species within a nematode community.© 2009 Blackwell Publishing Ltd.

Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaurnarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio, and extractable P content. Archaeal community composition and diversity were correlated to pH value, exchangeable Fe content, water content, and total N. The distribution of bacterial and archaeal taxa involved in biological N cycle indicated functional shifts of the cycle during conversion of rainforest to plantations.

Despite decades of research, the ecological determinants of microbial diversity remain poorly understood. Here, we test two alternative hypotheses concerning the factors regulating fungal diversity in soil. The first states that higher levels of plant detritus production increase the supply of limiting resources (i.e. organic substrates) thereby increasing fungal diversity. Alternatively, greater plant diversity increases the range of organic substrates entering soil, thereby increasing the number of niches to be filled by a greater array of heterotrophic fungi. These two hypotheses were simultaneously examined in experimental plant communities consisting of one to 16 species that have been maintained for a decade. We used ribosomal intergenic spacer analysis (RISA), in combination with cloning and sequencing, to quantify fungal community composition and diversity within the experimental plant communities. We used soil microbial biomass as a temporally integrated measure of resource supply. Plant diversity was unrelated to fungal diversity, but fungal diversity was a unimodal function of resource supply. Canonical correspondence analysis (CCA) indicated that plant diversity showed a relationship to fungal community composition, although the occurrence of RISA bands and operational taxonomic units (OTUs) did not differ among the treatments. The relationship between fungal diversity and resource availability parallels similar relationships reported for grasslands, tropical forests, coral reefs, and other biotic communities, strongly suggesting that the same underlying mechanisms determine the diversity of organisms at multiple scales.

The composition and distribution of ground-dwelling spider were investigated using small plot direct searching method to assess the impact of forest type and habitat management on spider diversity. Six forest types in Xishuangbanna, Yunnan Province, southwestern China were surveyed, <I>i.e.</I>, the tropical seasonal rain forest, limestone tropical seasonal rain forest, tropical montane evergreen broad-leaved forest, artificial forest, rubber-tea community and rubber plantation. A total of 18 plots (three repetitions for each forest type) were surveyed during three field trips in December 2006, March and July 2007. The relationships between forest type and spider diversity were explored using canonical correspondence analysis (CCA). A total of 9 849 individual spiders were collected from various habitats, of which 3 119 are identifiable adults representing 30 families. The most abundant families of ground-dwelling spider are Pholcidae, Linyphiidae, Theridiidae and Mysmenidae (62.2% of total species counts). Of the six forest types, 24 families were collected from the tropical seasonal rain forest including two endemic families; 22 families were collected from the limestone tropical seasonal rain forest; 22 families were collected from the tropical montane evergreen broad-leaved forest including two endemic families; 20 families were collected from the artificial forest; 21 families were collected from the rubber-tea community; and 19 families were collected from the rubber plantation including one endemic family. There are four families (13.3% of the total 30 families recorded) endemic to two types of rain forest, six families (20.0%) endemic to three types of natural forest, and one family (3.3%) endemic to plantations. Abundance of ground-dwelling spider in the tropical seasonal rain forest is significant higher than the remaining five types of forest. Shannon-Wiener (H′) index and Margalef index (Dmg) in the rubber plantation are significant lower than the three types of natural forest, and Pielou index (J) is also the lowest in the rubber plantation. The results of CCA and cluster analysis indicated that natural forests and plantations are well differentiated. In the group of natural forests, the tropical seasonal rain forest plots are well separated from two types of secondary forest plots. In the other group, the rubber plantation plots are well separated from the artificial forest and the rubber-tea community plots. The results suggested that: (1) human-management has an strong impact on ground-dwelling spider composition; (2) spider diversity decreases along with the increase of anthropogenic disturbance; and (3) reducing anthropogenic disturbance and increasing plant community diversity (<I>e.g.</I>, plant tea tree in rubber plantation) is a meaningful way to conserve and restore biodiversity.