Bacterial community shifts in organically perturbed sediments

Bacterial abundance, diversity and sediment function were investigated in organically perturbed sediments under Tasmanian salmon (Salmo salar) farms and adjacent reference sites. Bacterial numbers increased as farming and organic loading progressed through the farm stocking cycle and declined during the fallow period, although not to prestocking levels. Bacterial numbers ranged between approximately 2 x 10(8) and 3 x 10(9) cells per gram of sediment and were higher at cage sites than reference sites. Microelectrode and respiration data also demonstrated a clear effect of organic loading on sediments. Denaturing gradient gel electrophoresis (DGGE) showed that bacterial communities shifted both in response to farm loading and its cessation. A seasonal effect on microbial communities was also evident. Although bacterial communities did shift again during the fallowing period, this shift was not necessarily a return to preloading communities. The complexity of community shifts may be affected by the vast functional redundancy of bacterial groups. All bacterial communities, including those at reference sites, were highly dynamic. Respiration studies of amended sediments indicated that fish farm sediments were at least as resilient and diverse as reference site communities. The results of this study indicate that the functional redundancy of highly complex bacterial communities contributes to their robustness. The relationship between diversity and stability in bacterial communities remains unclear and requires further investigation before an understanding of bacterial response to perturbation is possible.     

太行山猕猴国家自然保护区木本植物群落结构和空间分布特征

多样化的森林群落为植物生长提供了不同的微生境。然而，物种在不同类型森林群落中是呈随机分布还是生态专化仍有待阐明。基于不同优势物种群落在太行山猕猴国家自然保护区建立了4个1 hm²（100 m×100 m）森林动态监测样地，采用Kruskal-Wallis方法、Betadisper检验分析不同群落间的物种组成和结构差异，利用相关网络和指示种分析探索物种-群落间的关系。结果表明，不同群落间木本植物的多度、丰富度和物种组成存在显著差异；共有5种物种同时出现在四个群落中，有43.82%（39/89）的物种分布在两个或两个以上的群落中；网络分析结果显示，物种与群落之间的连接指数为41.29%，专化指数为60.89%；指示种分析显示不同植物群落间指示物种不同。了解了太行山猕猴国家自然保护区不同群落的物种组成和群落结构特征。研究结果同时表明，木本植物在不同群落中的分布具有较高的专化特征。希望本研究能为该区域木本植物多样性维持机制的理解和物种保护提供一定参考。     

Spatial connectivity and boundary patterns in coastal dune vegetation in the Circeo National Park,Central Italy

Abstract. Distribution patterns of coastal sand dune plant communities in the Circeo National Park (Central Italy) are quantified and compared by measuring spatial connectivity and richness of community boundaries along the dune profile. The purpose of this study is: (1) to evaluate patchiness and frequency of spatial links between communities; (2) to identify the communities most sensitive to disturbance; and (3) to predict probable changes due to modification of spatial zonation. Data were obtained using belt transects across the Holocene coastal dune zone. Vegetation zonation from the seashore to the foredune slacks is analysed in relation to chorological, phytosociological and life‐form types. We found that under relatively undisturbed environmental conditions communities formed a sequence (communities 1 to 7), with the exception of a replacement community, which occupied gaps in the perennial vegetation. The spatial distribution of some communities was reduced as a consequence of disturbance; others became fragmented in small patches or even disappeared. In coastal environments with strong, complex gradients, the existence of certain communities depends on specific links (neighbourhood effects) and high connectivity values do not indicate better conservation conditions.     

Evolution in metacommunities

A metacommunity can be defined as a set of communities that are linked by migration, and extinction and recolonization. In metacommunities, evolution can occur not only by processes that occur within communities such as drift and individual selection, but also by among-community processes, such as divergent selection owing to random differences among communities in species composition, and group and community-level selection. The effect of these among-community-level processes depends on the pattern of migration among communities. Migrating units may be individuals (migrant pool model), groups of individuals (single-species propagule pool model) or multi-species associations (multi-species propagule pool model). The most interesting case is the multi-species propagule pool model. Although this pattern of migration may a priori seem rare, it becomes more plausible in small well-defined 'communities' such as symbiotic associations between two or a few species. Theoretical models and experimental studies show that community selection is potentially an effective evolutionary force. Such evolution can occur either through genetic changes within species or through changes in the species composition of the communities. Although laboratory studies show that community selection can be important, little is known about how important it is in natural populations.     

Species richness in tropical fresh waters of Australia

General ecological expectations about the relationship between latitude and species richness are that at low latitudes (the tropics) species richness is greater than at higher latitudes (temperate and polar regions). Recent work suggests that this may not be the case for several habitat types and biological groups in Australia. Results are conflicting: on present evidence (admittedly sparse) it appears that in Australian tropical fresh waters species richness is generally depressed in zooplankton and littoral microfaunal communities, but not in macroinvertebrate communities in typical streams and in fish communities (and perhaps also in amphibian and reptile communities). The situation is indeterminate for tropical phytoplankton and macrophyte communities.     

Relationship between Degree of Dominance and Species Richness in Grass Communities with Different Productivities

The aim of this study is to test the assumption that the relationship between the degree of dominance and local species richness may be different in grass communities with different productivities. Alpine, subalpine, and low-mountain grasslands, as well as subalpine mires, alpine communities of low-snow habitats and those with long-term snow cover, steppe communities, and the grass layer of low-mountain forest communities of the Western Caucasus and Ciscaucasia, are used as objects of research. The data on the phytomass of 419 plots with an area of 0.25 m² are studied. The results show that, the higher the mean productivity of communities is, the closer the relationship between the degree of dominance and species richness is, and the closest relationship is observed in meadow communities. Possible causes of these relationships are considered. It is reasonably suggested that this may be due to the features of the organization of plant communities with high and low productivity (in particular, high or low intensity of interspecific competition).     

Communities of arbuscular mycorrhizal fungi and bacteria in the rhizosphere of Caragana korshinkii and Hippophae rhamnoides in Zhifanggou watershed

The process of ecological restoration and reconstruction in Zhifanggou watershed forms a special ecosystem on the Loess Plateau. Little is known about the communities of arbuscular mycorrhizal fungi (AMF) and bacteria in this ecosystem. The aim of this study was to analyze the communities of AMF and bacteria, and their relationship in the rhizosphere of Caragana korshinkii and Hippophae rhamnoides in Zhifanggou watershed. Soil samples were collected from Zhifanggou watershed. The communities of AMF and bacteria were analyzed by using nested PCR of rDNA fragments and denaturing gradient gel electrophoresis (DGGE). Diversity analysis revealed that the bacterial Shannon diversity index was higher than that of AMF, and the AMF and bacterial Shannon diversity index in the rhizosphere of H. rhamnoides was higher than that of C. korshinkii. Principal component analysis (PCA) revealed that host plant had a significant influence on the bacterial community structure, but no strict specificity with AMF. Correlation analysis showed that the AMF communities had a significant positive correlation with the bacterial communities, and that indicated a significant effect of AMF on bacteria.     

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds

Microbial communities transform nitrogen (N) compounds, thereby regulating the availability of N in soil. The N cycle is defined by interacting microbial functional groups, as inorganic N‐products formed in one process are the substrate in one or several other processes. The nitrification pathway is often a two‐step process in which bacterial or archaeal communities oxidize ammonia to nitrite, and bacterial communities further oxidize nitrite to nitrate. Little is known about the significance of interactions between ammonia‐oxidizing bacteria (AOB) and archaea (AOA) and nitrite‐oxidizing bacterial communities (NOB) in determining the spatial variation of overall nitrifier community structure. We hypothesize that nonrandom associations exist between different AO and NOB lineages that, along with edaphic factors, shape field‐scale spatial patterns of nitrifying communities. To address this, we sequenced and quantified the abundance of AOA, AOB, and Nitrospira and Nitrobacter NOB communities across a 44‐hectare site with agricultural fields. The abundance of Nitrobacter communities was significantly associated only with AOB abundance, while that of Nitrospira was correlated to AOA. Network analysis and geostatistical modelling revealed distinct modules of co‐occurring AO and NOB groups occupying disparate areas, with each module dominated by different lineages and associated with different edaphic factors. Local communities were characterized by a high proportion of module‐connecting versus module‐hub nodes, indicating that nitrifier assemblages in these soils are shaped by fluctuating conditions. Overall, our results demonstrate the utility of network analysis in accounting for potential biotic interactions that define the niche space of nitrifying communities at scales compatible to soil management.     

Local climate mediates spatial and temporal variation in carabid beetle communities in three forests in Mount Odaesan,Korea

1. Global environmental change can dramatically alter the composition of floral and faunal communities, and elucidating the mechanisms underlying this process is important for predicting its outcomes. Studies on global climate change have mostly focused on statistical summaries within wide spatial and temporal scales; less attention has been paid to variability in microclimates at narrower spatial and temporal scales. 2. The microclimate is the suite of climatic conditions measured in a local area. Environmental variables at the microclimatic scale can be critical for the ecology of organisms inhabiting each area. The effect of spatial and temporal changes in the microclimate on the ecology of carabid beetle communities in three sites on Mount Odaesan, Korea was examined. 3. Carabid beetle communities and quantified site‐specific environmental factors from measurements of air temperature, air humidity, light intensity and soil temperature over 5 years (2010–2015) were surveyed. 4. It was found that microclimatic variables and the patterns of temporal changes in carabid beetle communities differed between the three sites within the single mountain system. Microclimatic variables influencing temporal changes in beetle communities also differed between the sites. Therefore, it is suggested that variation in local microclimates affects spatial and temporal variation in carabid beetle communities at a local scale. 5. The present results demonstrate the importance of regular surveys of communities at local scales. Such surveys are expected to reveal an additional fraction of variation in communities and underlying processes that have been overlooked in studies of global community patterns and change.     

Species abundance distribution and dynamics in two locally coupled communities

This study considered a model for species abundance dynamics in two local community (or islands) connected to a regional metacommunity. The model was analyzed using continuous probabilistic technique that employs Kolmogorov-Fokker-Planck forward equation to derive the probability density of the species abundance in the two local communities. Using this technique, we proposed a classification for the species abundance dynamics in the local communities. This classification was made based on such characteristics as immigration intensity, species representation in the metacommunity and the size of local communities. We further distinguished several different scenarios for species abundance dynamics using different ecological characteristics such as species persistence, extinction and monodominance in one or both local communities. The similarity of the species abundance distributions between the two local communities was studied using the correlation coefficient between species abundances in two local communities. The correlation is a function of migration rates between local communities and between local and metacommunity. Immigration between local communities drives the homogenization of the local communities, while immigration from the metacommunity will differentiate them. This community subdivision model provides useful insights for studying the effect of landscape fragmentation on species diversity.     

Dispersal and life span spectra in plant communities: a key to safe site dynamics, species coexistence and conservation

Dispersal and life span of individual plant species within five plant communities were assessed to obtain a characterization of these communities in this respect. Such a characterization is important in the context of restoration and maintenance. The most frequent species of five communities were ranked in eight classes according to their level of seed dispersal capability, their seed bank formation (dispersal in time and space) and their individual life span. In the communities, all eight classes were found, but communities differed in the distribution of the species over the classes.
A theoretical framework was constructed to use the level of specialization of plant species in terms of dispersal in space and time, and life span, to define the characteristics of safe site dynamics within communities. Following simple rules, the relative reliability of the occurrence of safe sites in space and time was defined. After that, the relative reliability of the habitat was linked to the best fitting combination of trait specialization level. Having defined this link, communities could be characterized in a comparative way by their level and pattern of reliability of the opportunities for recruitment in space and time.
The meaning of the coexistence of a range of trait combinations in one community was discussed. It was postulated that habitat reliability can explain this by assuming that the habitat of the community is part of a larger system, or consists of several “subsystems”. These insights need to be considered in nature conservation. Succession and also specializations beyond the scope of dispersal and life span may influence the occurrence of species in a seemingly unfit habitat (for instance the occurrence of semi parasitic annuals in a community of perennials, because they use the perennial root system of other species). Finally, the meaning of safe site reliability in space and time in the context of restoration of communities was discussed. The reliability in space and time may be different today from that of the past, which restricts the feasibility of restoration of communities.     

The influence of stream habitat and water quality on macroinvertebrate communities in degraded streams of northwest Mississippi

Streams in the loess hills of northwest Mississippi have undergone dramatic physical changes since European settlement and both physical and water quality processes may play a role in influencing biotic communities of these stream systems. The objectives of this study were to identify the response of macroinvertebrate taxa to water quality and habitat parameters in streams of northwest Mississippi, examine the efficacy of an a priori classification system of stream channel evolution and condition class using macroinvertebrate communities, and examine short-term (<2 yr) temporal variation of macroinvertebrate communities. Separation of sites based on four condition classifications was not distinct. However, best attainable sites did plot together in an ordination analysis suggesting similarity in macroinvertebrate communities for least disturbed sites. Similarly, for stage of channel evolution, sites characterized by lack of bank failure and sinuous fluvial processes had relatively similar macroinvertebrate communities. Ordination analysis also indicated high temporal variation of macroinvertebrate communities. Reference sites (best attainable and stable sites) had more similar communities between years than unstable and impacted sites. Results of this study: (1) suggest total solids, total phosphorus concentration, percent substrate as sand, ammonia concentration, and conductivity were important variables for structuring stream macroinvertebrate communities in northwest Mississippi, (2) identify potential indicator taxa for assessing such streams based on water quality and physical habitat, (3) provide support for current a priori site classifications at the best attainable (least impacted) category relative to the macroinvertebrate communities, and (4) demonstrate that between-year variation is an important factor when assessing streams of north Mississippi and this variability may be related to the degree of stream degradation.     

Shifts in root-associated microbial communities of Typha latifolia growing in naphthenic acids and relationship to plant health

Naphthenic acids (NAs) are a complex mixture of organic acid compounds released during the extraction of crude oil from oil sands operations. The accumulation of toxic NAs in tailings pond water (TPW) is of significant environmental concern, and phytoremediation using constructed wetlands is one remediation option being assessed. Since root-associated microorganisms are an important factor during phytoremediation of organic compounds, this study investigated the impact of NAs on the microbial communities associated with the macrophyte Typha latifolia (cattail). Denaturing gradient gel electrophoresis revealed that the impact of NAs on microbial communities was niche dependent, with endophytic communities being the most stable and bulk water communities being the least stable. The type of NA used was significant to microbial response, with commercial NAs causing greater adverse changes than TPW NAs. In general, plant beneficial bacteria such as diazotrophs were favoured in cattails grown in TPW NAs, while potentially deleterious bacteria such as denitrifying Dechlorospirillum species increased in commercial NA treatments. These findings suggest that NAs may affect plant health by impacting root-associated microbial communities. A better understanding of these impacts may allow researchers to optimize those microbial communities that support plant health, and thus further optimize wetland treatment systems.     

Community Structures in Bipartite Networks: A Dual-Projection Approach

Identifying communities or clusters in networked systems has received much attention across the physical and social sciences. Most of this work focuses on single layer or one-mode networks, including social networks between people or hyperlinks between websites. Multilayer or multi-mode networks, such as affiliation networks linking people to organizations, receive much less attention in this literature. Common strategies for discovering the community structure of multi-mode networks identify the communities of each mode simultaneously. Here I show that this combined approach is ineffective at discovering community structures when there are an unequal number of communities between the modes of a multi-mode network. I propose a dual-projection alternative for detecting communities in multi-mode networks that overcomes this shortcoming. The evaluation of synthetic networks with known community structures reveals that the dual-projection approach outperforms the combined approach when there are a different number of communities in the various modes. At the same time, results show that the dual-projection approach is as effective as the combined strategy when the number of communities is the same between the modes.     

Community relaxation in fragmented landscapes: the relation between species richness, area and age

Estimates of species loss due to habitat destruction are normally based on calculations employing the species–area relation, S = cA ^z . The validity of this approach is based on the assumption that the value of the exponent ( z ) defining the slope of the species–area relation in nonfragmented communities is at a steady state and that z is thus a constant. However, departure from such an assumption renders this approach unreliable. Here I report the results from a natural field experiment using "model" bryophyte-based microlandscapes designed to follow the species richness dynamics of microarthropod communities postfragmentation. Community isolation due to fragmentation initiated a delayed community relaxation process and resulted in substantial local extinction. Over the period of the experiment z declined in the control communities and yet remained fairly stable in the fragmented communities. I conclude that predictions of species loss due to habitat fragmentation that do not take into account the fact that often z may not be a constant may lead to error-prone predictions of future species loss.     

Grazing and the vanishing complexity of plant association networks in grasslands

Interactions are key drivers of the functioning and fate of plant communities. A traditional way to measure them is to use pairwise experiments, but such experiments do not scale up to species-rich communities. For those, using association networks based on spatial patterns may provide a more realistic approach. While this method has been successful in abiotically-stressed environments (alpine and arid ecosystems), it is unclear how well it generalizes to other types of environments. We help fill this knowledge gap by documenting how the structure of plant communities changes in a Mediterranean dry grassland grazed by sheep using plant spatial association networks. We investigated how the structure of these networks changed with grazing intensity to show the effect of biotic disturbance on community structure. We found that these grazed grassland communities were mostly dominated by negative associations, suggesting a dominance of interference over facilitation regardless of the disturbance level. The topology of the networks revealed that the number of associations were not evenly-distributed across species, but rather that a small subset of species established most negative associations under low grazing conditions. All these aspects of spatial organization vanished under high level of grazing as association networks became more similar to null expectations. Our study shows that grazed herbaceous plant communities display a highly non-random organization that responds strongly to disturbance and can be measured through association networks. This approach thus appears insightful to test general hypotheses about plant communities, and in particular understand how anthropogenic perturbations affect the organization of ecological communities.     

A Shadowing Problem in the Detection of Overlapping Communities: Lifting the Resolution Limit through a Cascading Procedure

Community detection is the process of assigning nodes and links in significant communities (e.g. clusters, function modules) and its development has led to a better understanding of complex networks. When applied to sizable networks, we argue that most detection algorithms correctly identify prominent communities, but fail to do so across multiple scales. As a result, a significant fraction of the network is left uncharted. We show that this problem stems from larger or denser communities overshadowing smaller or sparser ones, and that this effect accounts for most of the undetected communities and unassigned links. We propose a generic cascading approach to community detection that circumvents the problem. Using real and artificial network datasets with three widely used community detection algorithms, we show how a simple cascading procedure allows for the detection of the missing communities. This work highlights a new detection limit of community structure, and we hope that our approach can inspire better community detection algorithms.     

Response of microbial community structure to microbial plugging in a mesothermic petroleum reservoir in China

Microbial plugging, a microbial enhancement of oil recovery (MEOR) technique, has been applied in a candidate oil reservoir of Daqing Oil Field (China). The goal of this study is to monitor the survival of injected bacteria and reveal the response of microbial communities in field trial of microbial plugging through injection of selected microbial culture broth and nutrients. Culture-dependent enrichment and culture-independent 16S rDNA clone library methods were used. The results show that it was easy to activate targeted biopolymer-producing bacteria in a laboratory environment, and it was difficult for injected exogenous bacteria to survive. In addition, microbial communities in the oil reservoir also changed before and after the field trial. However, microbial communities, activated by fermentative medium for biopolymer-producing bacteria, appeared to show greater differences in the laboratory than in the natural reservoir. It was concluded that microbial populations monitoring was important to MEOR; results of response of microbial communities could provide a guide for the future field trials.     

Microbial diversity and community structure in Fynbos soil

The Fynbos biome in South Africa is renowned for its high plant diversity and the conservation of this area is particularly important for the region. This is especially true in the case of endangered vegetation types on the lowlands such as Sand Fynbos, of which only small fragments remain. The question is thus whether the diversity of the above‐ground flora is mirrored in the below‐ground microbial communities. In order to determine the relationship of the above‐ and below‐ground communities, the soil community composition of both fungal and bacterial groups in Sand Fynbos was characterized over space and time. A molecular approach was used based on the isolation of total soil genomic DNA and automated ribosomal intergenic spacer analysis of bacterial and fungal communities. Soil from four different sites was compared to resolve the microbial diversity of eubacterial and fungal groups on a local (alpha diversity) scale as well as a landscape scale (beta diversity). The community structures from different sites were compared and found to exhibit strong spatial patterns which remained stable over time. The plant community data were compared with the fungal and the bacterial communities. We concluded that the microbial communities in the Sand Fynbos are highly diverse and closely linked to the above‐ground floral communities.     

Diversity of Planktonic and Attached Bacterial Communities in a Phenol-Contaminated Sandstone Aquifer

Polluted aquifers contain indigenous microbial communities with the potential for in situ bioremediation. However, the effect of hydrogeochemical gradients on in situ microbial communities (especially at the plume fringe, where natural attenuation is higher) is still not clear. In this study, we used culture-independent techniques to investigate the diversity of in situ planktonic and attached bacterial communities in a phenol-contaminated sandstone aquifer. Within the upper and lower plume fringes, denaturing gradient gel electrophoresis profiles indicated that planktonic community structure was influenced by the steep hydrogeochemical gradient of the plume rather than the spatial location in the aquifer. Under the same hydrogeochemical conditions (in the lower plume fringe, 30 m below ground level), 16S rRNA gene cloning and sequencing showed that planktonic and attached bacterial communities differed markedly and that the attached community was more diverse. The 16S rRNA gene phylogeny also suggested that a phylogenetically diverse bacterial community operated at this depth (30 mbgl), with biodegradation of phenolic compounds by nitrate-reducing Azoarcus and Acidovorax strains potentially being an important process. The presence of acetogenic and sulphate-reducing bacteria only in the planktonic clone library indicates that some natural attenuation processes may occur preferentially in one of the two growth phases (attached or planktonic). Therefore, this study has provided a better understanding of the microbial ecology of this phenol-contaminated aquifer, and it highlights the need for investigating both planktonic and attached microbial communities when assessing the potential for natural attenuation in contaminated aquifers.