Counting on β-Diversity to Safeguard the Resilience of Estuaries

Coastal ecosystems are often stressed by non-point source and cumulative effects that can lead to local-scale community homogenisation and a concomitant loss of large-scale ecological connectivity. Here we investigate the use of β-diversity as a measure of both community heterogeneity and ecological connectivity. To understand the consequences of different environmental scenarios on heterogeneity and connectivity, it is necessary to understand the scale at which different environmental factors affect β-diversity. We sampled macrofauna from intertidal sites in nine estuaries from New Zealand’s North Island that represented different degrees of stress derived from land-use. We used multiple regression models to identify relationships between β-diversity and local sediment variables, factors related to the estuarine and catchment hydrodynamics and morphology and land-based stressors. At local scales, we found higher β-diversity at sites with a relatively high total richness. At larger scales, β-diversity was positively related to γ-diversity, suggesting that a large regional species pool was linked with large-scale heterogeneity in these systems. Local environmental heterogeneity influenced β-diversity at both local and regional scales, although variables at the estuarine and catchment scales were both needed to explain large scale connectivity. The estuaries expected a priori to be the most stressed exhibited higher variance in community dissimilarity between sites and connectivity to the estuary species pool. This suggests that connectivity and heterogeneity metrics could be used to generate early warning signals of cumulative stress.     

Large Spatial Scale Variability in Bathyal Macrobenthos Abundance,Biomass, α- and β-Diversity along the Mediterranean Continental Margin

The large-scale deep-sea biodiversity distribution of the benthic fauna was explored in the Mediterranean Sea, which can be seen as a miniature model of the oceans of the world. Within the framework of the BIOFUN project (“Biodiversity and Ecosystem Functioning in Contrasting Southern European Deep-sea Environments: from viruses to megafauna”), we investigated the large spatial scale variability (over >1,000 km) of the bathyal macrofauna communities that inhabit the Mediterranean basin, and their relationships with the environmental variables. The macrofauna abundance, biomass, community structure and functional diversity were analysed and the α-diversity and β-diversity were estimated across six selected slope areas at different longitudes and along three main depths. The macrobenthic standing stock and α-diversity were lower in the deep-sea sediments of the eastern Mediterranean basin, compared to the western and central basins. The macrofaunal standing stock and diversity decreased significantly from the upper bathyal to the lower bathyal slope stations. The major changes in the community composition of the higher taxa and in the trophic (functional) structure occurred at different longitudes, rather than at increasing water depth. For the β-diversity, very high dissimilarities emerged at all levels: (i) between basins; (ii) between slopes within the same basin; and (iii) between stations at different depths; this therefore demonstrates the high macrofaunal diversity of the Mediterranean basins at large spatial scales. Overall, the food sources (i.e., quantity and quality) that characterised the west, central and eastern Mediterranean basins, as well as sediment grain size, appear to influence the macrobenthic standing stock and the biodiversity along the different slope areas.     

Additive Diversity Partitioning of Fish in a Caribbean Coral Reef Undergoing Shift Transition

Shift transitions in dominance on coral reefs from hard coral cover to fleshy macroalgae are having negative effects on Caribbean coral reef communities. Data on spatiotemporal changes in biodiversity during these modifications are important for decision support for coral reef biodiversity protection. The main objective of this study is to detect the spatiotemporal patterns of coral reef fish diversity during this transition using additive diversity-partitioning analysis. We examined α, β and γ fish diversity from 2000 to 2010, during which time a shift transition occurred at Mahahual Reef, located in Quintana Roo, Mexico. Data on coral reef fish and benthic communities were obtained from 12 transects per geomorphological unit (GU) in two GUs (reef slope and terrace) over six years (2000, 2005, 2006, 2007, 2008, 2010). Spatial analysis within and between the GUs indicated that the γ-diversity was primarily related to higher β-diversity. Throughout the six study years, there were losses of α, β and γ-diversity associated spatially with the shallow (reef slope) and deeper (reef terrace) GUs and temporally with the transition in cover from mound corals to fleshy macroalgae and boulder corals. Despite a drastic reduction in the number of species over time, β-diversity continues to be the highest component of γ-diversity. The shift transition had a negative effect on α, β and γ-diversity, primarily by impacting rare species, leading a group of small and less vulnerable fish species to become common and an important group of rare species to become locally extinct. The maintenance of fish heterogeneity (β-diversity) over time may imply the abetment of vulnerability in the face of local and global changes.     

Spatial and Temporal Patterns in Macrofaunal Diversity Components Relative to Sea Floor Landscape Structure

We examined temporal changes in macrofaunal α- and β-diversity over several spatial scales (within patches, among patches, across landscapes and across regions) in Long Island Sound on the northeast USA coast. Regional ε-diversity was estimated at 144 taxa, however γ-diversity fluctuated over time as did α- and β-diversity components. Based on additive partitioning, patch- and region-scale β-diversity components generally had the highest contributions to γ-diversity; lower percentages were found at within-patch and landscape scales. Multiplicative diversity partitioning indicated highest species turnover at within- and among patch scales. For all partition results, within-patch and patch-scale β-diversity increased sharply when hypoxia impacted benthic communities. Spatial variation in diversity components can be attributed to the collection of different patch types at varying spatial scales and their associated habitats across the benthic landscapes, as well as gradients in depth and other estuarine-scale characteristics. Temporal variation in diversity components across spatial scales may be related to seasonal changes in habitat heterogeneity, species population dynamics, and seasonal disturbances. Rare species were significant and temporally consistent components of macrofaunal diversity patterns over different spatial scales. Our findings agree with other marine and terrestrial studies that show diversity components vary significantly over different spatial scales and the importance of habitat/landscape heterogeneity in supporting diversity. However, our results indicate that the relative contributions of scale-specific β-diversity components can also change significantly over time. Thus, studies of diversity patterns across patches and landscapes based on data collected at one time, or assembled into a single data set from different times, may not capture the full suite of diversity patterns that occur over varying spatial scales and any time-specific determinants of those patterns. Many factors that shape and maintain sedimentary communities vary temporally, and appear to play an important role in determining and maintaining macrofaunal diversity over different spatial scales.     

Elevational Gradients in β-Diversity Reflect Variation in the Strength of Local Community Assembly Mechanisms across Spatial Scales

Despite long-standing interest in elevational-diversity gradients, little is known about the processes that cause changes in the compositional variation of communities (β-diversity) across elevations. Recent studies have suggested that β-diversity gradients are driven by variation in species pools, rather than by variation in the strength of local community assembly mechanisms such as dispersal limitation, environmental filtering, or local biotic interactions. However, tests of this hypothesis have been limited to very small spatial scales that limit inferences about how the relative importance of assembly mechanisms may change across spatial scales. Here, we test the hypothesis that scale-dependent community assembly mechanisms shape biogeographic β-diversity gradients using one of the most well-characterized elevational gradients of tropical plant diversity. Using an extensive dataset on woody plant distributions along a 4,000-m elevational gradient in the Bolivian Andes, we compared observed patterns of β-diversity to null-model expectations. β-deviations (standardized differences from null values) were used to measure the relative effects of local community assembly mechanisms after removing sampling effects caused by variation in species pools. To test for scale-dependency, we compared elevational gradients at two contrasting spatial scales that differed in the size of local assemblages and regions by at least an order of magnitude. Elevational gradients in β-diversity persisted after accounting for regional variation in species pools. Moreover, the elevational gradient in β-deviations changed with spatial scale. At small scales, local assembly mechanisms were detectable, but variation in species pools accounted for most of the elevational gradient in β-diversity. At large spatial scales, in contrast, local assembly mechanisms were a dominant force driving changes in β-diversity. In contrast to the hypothesis that variation in species pools alone drives β-diversity gradients, we show that local community assembly mechanisms contribute strongly to systematic changes in β-diversity across elevations. We conclude that scale-dependent variation in community assembly mechanisms underlies these iconic gradients in global biodiversity.     

Submarine canyons: hotspots of benthic biomass and productivity in the deep sea

Submarine canyons are dramatic and widespread topographic features crossing continental and island margins in all oceans. Canyons can be sites of enhanced organic-matter flux and deposition through entrainment of coastal detrital export, dense shelf-water cascade, channelling of resuspended particulate material and focusing of sediment deposition. Despite their unusual ecological characteristics and global distribution along oceanic continental margins, only scattered information is available about the influence of submarine canyons on deep-sea ecosystem structure and productivity. Here, we show that deep-sea canyons such as the Kaikoura Canyon on the eastern New Zealand margin (42°01′ S, 173°03′ E) can sustain enormous biomasses of infaunal megabenthic invertebrates over large areas. Our reported biomass values are 100-fold higher than those previously reported for deep-sea (non-chemosynthetic) habitats below 500 m in the ocean. We also present evidence from deep-sea-towed camera images that areas in the canyon that have the extraordinary benthic biomass also harbour high abundances of macrourid (rattail) fishes likely to be feeding on the macro- and megabenthos. Bottom-trawl catch data also indicate that the Kaikoura Canyon has dramatically higher abundances of benthic-feeding fishes than adjacent slopes. Our results demonstrate that the Kaikoura Canyon is one of the most productive habitats described so far in the deep sea. A new global inventory suggests there are at least 660 submarine canyons worldwide, approximately 100 of which could be biomass hotspots similar to the Kaikoura Canyon. The importance of such deep-sea canyons as potential hotspots of production and commercial fisheries yields merits substantial further study.     

Biodiversity Patterns along Ecological Gradients: Unifying β-Diversity Indices

Ecologists have developed an abundance of conceptions and mathematical expressions to define β-diversity, the link between local (α) and regional-scale (γ) richness, in order to characterize patterns of biodiversity along ecological (i.e., spatial and environmental) gradients. These patterns are often realized by regression of β-diversity indices against one or more ecological gradients. This practice, however, is subject to two shortcomings that can undermine the validity of the biodiversity patterns. First, many β-diversity indices are constrained to range between fixed lower and upper limits. As such, regression analysis of β-diversity indices against ecological gradients can result in regression curves that extend beyond these mathematical constraints, thus creating an interpretational dilemma. Second, despite being a function of the same measured α- and γ-diversity, the resultant biodiversity pattern depends on the choice of β-diversity index. We propose a simple logistic transformation that rids beta-diversity indices of their mathematical constraints, thus eliminating the possibility of an uninterpretable regression curve. Moreover, this transformation results in identical biodiversity patterns for three commonly used classical beta-diversity indices. As a result, this transformation eliminates the difficulties of both shortcomings, while allowing the researcher to use whichever beta-diversity index deemed most appropriate. We believe this method can help unify the study of biodiversity patterns along ecological gradients.     

Are Organic Falls Bridging Reduced Environments in the Deep Sea? - Results from Colonization Experiments in the Gulf of Cádiz

Organic falls create localised patches of organic enrichment and disturbance where enhanced degradation is mediated by diversified microbial assemblages and specialized fauna. The view of organic falls as “stepping stones” for the colonization of deep-sea reducing environments has been often loosely used, but much remains to be proven concerning their capability to bridge dispersal among such environments. Aiming the clarification of this issue, we used an experimental approach to answer the following questions:Are relatively small organic falls in the deep sea capable of sustaining taxonomically and trophically diverse assemblages over demographically relevant temporal scales?Are there important depth- or site-related sources of variability for the composition and structure of these assemblages? Is the proximity of other reducing environments influential for their colonization?We analysed the taxonomical and trophic diversity patterns and partitioning (α- and β-diversity) of the macrofaunal assemblages recruited in small colonization devices with organic and inorganic substrata after 1-2 years of deployment on mud volcanoes of the Gulf of Cádiz. Our results show that small organic falls can sustain highly diverse and trophically coherent assemblages for time periods allowing growth to reproductive maturity, and successive generations of dominant species. The composition and structure of the assemblages showed variability consistent with their biogeographic and bathymetric contexts. However, the proximity of cold seeps had limited influence on the similarity between the assemblages of these two habitats and organic falls sustained a distinctive fauna with dominant substrate-specific taxa. We conclude that it is unlikely that small organic falls may regularly ensure population connectivity among cold seeps and vents. They may be a recurrent source of evolutionary candidates for the colonization of such ecosystems. However, there may be a critical size of organic fall to create the necessary intense and persistent reducing conditions for sustaining typical chemosymbiotic vent and seep organisms.     

Niche and metabolic principles explain patterns of diversity and distribution: theory and a case study with soil bacterial communities

The causes of biodiversity patterns are controversial and elusive due to complex environmental variation, covarying changes in communities, and lack of baseline and null theories to differentiate straightforward causes from more complex mechanisms. To address these limitations, we developed general diversity theory integrating metabolic principles with niche-based community assembly. We evaluated this theory by investigating patterns in the diversity and distribution of soil bacteria taxa across four orders of magnitude variation in spatial scale on an Antarctic mountainside in low complexity, highly oligotrophic soils. Our theory predicts that lower temperatures should reduce taxon niche widths along environmental gradients due to decreasing growth rates, and the changing niche widths should lead to contrasting α- and β-diversity patterns. In accord with the predictions, α-diversity, niche widths and occupancies decreased while β-diversity increased with increasing elevation and decreasing temperature. The theory also successfully predicts a hump-shaped relationship between α-diversity and pH and a negative relationship between α-diversity and salinity. Thus, a few simple principles explained systematic microbial diversity variation along multiple gradients. Such general theory can be used to disentangle baseline effects from more complex effects of temperature and other variables on biodiversity patterns in a variety of ecosystems and organisms.     

Temporal variation of β-diversity and assembly mechanisms in a bacterial metacommunity

The turnover of community composition across space, β-diversity, is influenced by different assembly mechanisms, which place varying weight on local habitat factors, such as environmental conditions and species interactions, and regional factors such as dispersal and history. Several assembly mechanisms may function simultaneously; however, little is known about how their importance changes over time and why. Here, we implemented a field survey where we sampled a bacterial metacommunity consisting of 17 rock pools located at the Swedish Baltic Sea coast at 11 occasions during 1 year. We determined to which extent communities were structured by different assembly mechanisms using variation partitioning and studied changes in β-diversity across environmental gradients over time. β-Diversity was highest at times of high overall productivity and environmental heterogeneity in the metacommunity, at least partly due to species sorting, that is, selection of taxa by the prevailing environmental conditions. In contrast, dispersal-driven assembly mechanisms were primarily detected at times when β-diversity was relatively low. There were no indications for strong and persistent differences in community composition or β-diversity between permanent and temporary pools, indicating that the physical disturbance regime is of relatively minor importance. In summary, our study clearly suggests that there are temporal differences in the relative importance of different assembly mechanisms related to abiotic factors and shows that the temporal variability of those factors is important for a more complete understanding of bacterial metacommunity dynamics.     

Additive Partitioning of Coral Reef Fish Diversity across Hierarchical Spatial Scales throughout the Caribbean

There is an increasing need to examine regional patterns of diversity in coral-reef systems since their biodiversity is declining globally. In this sense, additive partitioning might be useful since it quantifies the contribution of alpha and beta to total diversity across different scales. We applied this approach using an unbalanced design across four hierarchical scales (80 sites, 22 subregions, six ecoregions, and the Caribbean basin). Reef-fish species were compiled from the Reef Environmental Education Foundation (REEF) database and distributions were confirmed with published data. Permutation tests were used to compare observed values to those expected by chance. The primary objective was to identify patterns of reef-fish diversity across multiple spatial scales under different scenarios, examining factors such as fisheries and demographic connectivity. Total diversity at the Caribbean scale was attributed to β-diversity (nearly 62% of the species), with the highest β-diversity at the site scale. α¯-diversity was higher than expected by chance in all scenarios and at all studied scales. This suggests that fish assemblages are more homogenous than expected, particularly at the ecoregion scale. Within each ecoregion, diversity was mainly attributed to alpha, except for the Southern ecoregion where there was a greater difference in species among sites. β-components were lower than expected in all ecoregions, indicating that fishes within each ecoregion are a subsample of the same species pool. The scenario involving the effects of fisheries showed a shift in dominance for β-diversity from regions to subregions, with no major changes to the diversity patterns. In contrast, demographic connectivity partially explained the diversity pattern. β-components were low within connectivity regions and higher than expected by chance when comparing between them. Our results highlight the importance of ecoregions as a spatial scale to conserve local and regional coral reef-fish diversity.     

β-Diversity and Species Accumulation in Antarctic Coastal Benthos: Influence of Habitat,Distance and Productivity on Ecological Connectivity

High Antarctic coastal marine environments are comparatively pristine with strong environmental gradients, which make them important places to investigate biodiversity relationships. Defining how different environmental features contribute to shifts in β-diversity is especially important as these shifts reflect both spatio-temporal variations in species richness and the degree of ecological separation between local and regional species pools. We used complementary techniques (species accumulation models, multivariate variance partitioning and generalized linear models) to assess how the roles of productivity, bio-physical habitat heterogeneity and connectivity change with spatial scales from metres to 100''s of km. Our results demonstrated that the relative importance of specific processes influencing species accumulation and β–diversity changed with increasing spatial scale, and that patterns were never driven by only one factor. Bio-physical habitat heterogeneity had a strong influence on β-diversity at scales <290 km, while the effects of productivity were low and significant only at scales >40 km. Our analysis supports the emphasis on the analysis of diversity relationships across multiple spatial scales and highlights the unequal connectivity of individual sites to the regional species pool. This has important implications for resilience to habitat loss and community homogenisation, especially for Antarctic benthic communities where rates of recovery from disturbance are slow, there is a high ratio of poor-dispersing and brooding species, and high biogenic habitat heterogeneity and spatio-temporal variability in primary production make the system vulnerable to disturbance. Consequently, large areas need to be included within marine protected areas for effective management and conservation of these special ecosystems in the face of increasing anthropogenic disturbance.     

Spatial Diversity of Bacterioplankton Communities in Surface Water of Northern South China Sea

The South China Sea is one of the largest marginal seas, with relatively frequent passage of eddies and featuring distinct spatial variation in the western tropical Pacific Ocean. Here, we report a phylogenetic study of bacterial community structures in surface seawater of the northern South China Sea (nSCS). Samples collected from 31 sites across large environmental gradients were used to construct clone libraries and yielded 2,443 sequences grouped into 170 OTUs. Phylogenetic analysis revealed 23 bacterial classes with major components α-, β- and γ-Proteobacteria, as well as Cyanobacteria. At class and genus taxon levels, community structure of coastal waters was distinctively different from that of deep-sea waters and displayed a higher diversity index. Redundancy analyses revealed that bacterial community structures displayed a significant correlation with the water depth of individual sampling sites. Members of α-Proteobacteria were the principal component contributing to the differences of the clone libraries. Furthermore, the bacterial communities exhibited heterogeneity within zones of upwelling and anticyclonic eddies. Our results suggested that surface bacterial communities in nSCS had two-level patterns of spatial distribution structured by ecological types (coastal VS. oceanic zones) and mesoscale physical processes, and also provided evidence for bacterial phylogenetic phyla shaped by ecological preferences.     

Reproducibility and quantitation of amplicon sequencing-based detection

To determine the reproducibility and quantitation of the amplicon sequencing-based detection approach for analyzing microbial community structure, a total of 24 microbial communities from a long-term global change experimental site were examined. Genomic DNA obtained from each community was used to amplify 16S rRNA genes with two or three barcode tags as technical replicates in the presence of a small quantity (0.1% wt/wt) of genomic DNA from Shewanella oneidensis MR-1 as the control. The technical reproducibility of the amplicon sequencing-based detection approach is quite low, with an average operational taxonomic unit (OTU) overlap of 17.2%±2.3% between two technical replicates, and 8.2%±2.3% among three technical replicates, which is most likely due to problems associated with random sampling processes. Such variations in technical replicates could have substantial effects on estimating β-diversity but less on α-diversity. A high variation was also observed in the control across different samples (for example, 66.7-fold for the forward primer), suggesting that the amplicon sequencing-based detection approach could not be quantitative. In addition, various strategies were examined to improve the comparability of amplicon sequencing data, such as increasing biological replicates, and removing singleton sequences and less-representative OTUs across biological replicates. Finally, as expected, various statistical analyses with preprocessed experimental data revealed clear differences in the composition and structure of microbial communities between warming and non-warming, or between clipping and non-clipping. Taken together, these results suggest that amplicon sequencing-based detection is useful in analyzing microbial community structure even though it is not reproducible and quantitative. However, great caution should be taken in experimental design and data interpretation when the amplicon sequencing-based detection approach is used for quantitative analysis of the β-diversity of microbial communities.     

Temporal variability in soil microbial communities across land-use types

Although numerous studies have investigated changes in soil microbial communities across space, questions about the temporal variability in these communities and how this variability compares across soils have received far less attention. We collected soils on a monthly basis (May to November) from replicated plots representing three land-use types (conventional and reduced-input row crop agricultural plots and early successional grasslands) maintained at a research site in Michigan, USA. Using barcoded pyrosequencing of the 16S rRNA gene, we found that the agricultural and early successional land uses harbored unique soil bacterial communities that exhibited distinct temporal patterns. α-Diversity, the numbers of taxa or lineages, was significantly influenced by the sampling month with the temporal variability in α-diversity exceeding the variability between land-use types. In contrast, differences in community composition across land-use types were reasonably constant across the 7-month period, suggesting that the time of sampling is less important when assessing β-diversity patterns. Communities in the agricultural soils were most variable over time and the changes were significantly correlated with soil moisture and temperature. Temporal shifts in bacterial community composition within the successional grassland plots were less predictable and are likely a product of complex interactions between the soil environment and the more diverse plant community. Temporal variability needs to be carefully assessed when comparing microbial diversity across soil types and the temporal patterns in microbial community structure can not necessarily be generalized across land uses, even if those soils are exposed to the same climatic conditions.     

Quantifying Recent Ecological Changes in Remote Lakes of North America and Greenland Using Sediment Diatom Assemblages

Background

Although arctic lakes have responded sensitively to 20^th-century climate change, it remains uncertain how these ecological transformations compare with alpine and montane-boreal counterparts over the same interval. Furthermore, it is unclear to what degree other forcings, including atmospheric deposition of anthropogenic reactive nitrogen (Nr), have participated in recent regime shifts. Diatom-based paleolimnological syntheses offer an effective tool for retrospective assessments of past and ongoing changes in remote lake ecosystems.

Methodology/Principal Findings

We synthesized 52 dated sediment diatom records from lakes in western North America and west Greenland, spanning broad latitudinal and altitudinal gradients, and representing alpine (n = 15), arctic (n = 20), and forested boreal-montane (n = 17) ecosystems. Diatom compositional turnover (β-diversity) during the 20^th century was estimated using Detrended Canonical Correspondence Analysis (DCCA) for each site and compared, for cores with sufficiently robust chronologies, to both the 19^th century and the prior ∼250 years (Little Ice Age). For both arctic and alpine lakes, β-diversity during the 20^th century is significantly greater than the previous 350 years, and increases with both latitude and altitude. Because no correlation is apparent between 20^th-century diatom β-diversity and any single physical or limnological parameter (including lake and catchment area, maximum depth, pH, conductivity, [NO₃ ⁻], modeled Nr deposition, ambient summer and winter air temperatures, and modeled temperature trends 1948–2008), we used Principal Components Analysis (PCA) to summarize the amplitude of recent changes in relationship to lake pH, lake:catchment area ratio, modeled Nr deposition, and recent temperature trends.

Conclusions/Significance

The ecological responses of remote lakes to post-industrial environmental changes are complex. However, two regions reveal concentrations of sites with elevated 20^th-century diatom β-diversity: the Arctic where temperatures are increasing most rapidly, and mid-latitude alpine lakes impacted by high Nr deposition rates. We predict that remote lakes will continue to shift towards new ecological states in the Anthropocene, particularly in regions where these two forcings begin to intersect geographically.     

Primates as Predictors of Mammal Community Diversity in the Forest Ecosystems of Madagascar

The geographic distribution of species is the typical metric for identifying priority areas for conservation. Since most biodiversity remains poorly studied, a subset of charismatic species, such as primates, often stand as surrogates for total biodiversity. A central question is therefore, how effectively do primates predict the pooled species richness of other mammalian taxa? We used lemurs as indicator species to predict total non-primate mammal community richness in the forest ecosystems of Madagascar. We combine environmental and species occurrence data to ascertain the extent to which primate diversity can predict (1) non-primate mammal α-diversity (species richness), (2) non-primate complementarity, and (3) non-primate β-diversity (species turnover). Our results indicate that primates are effective predictors of non-primate mammal community diversity in the forest ecosystems of Madagascar after controlling for habitat. When individual orders of mammals are considered, lemurs effectively predict the species richness of carnivorans and rodents (but not afrosoricids), complementarity of rodents (but not carnivorans or afrosoricids), and all individual components of β-diversity. We conclude that lemurs effectively predict total non-primate community richness. However, surrogate species alone cannot achieve complete representation of biodiversity.     

The eukaryotic leading and lagging strand DNA polymerases are loaded onto primer-ends via separate mechanisms but have comparable processivity in the presence of PCNA

Saccharomyces cerevisiae DNA polymerase δ (Pol δ) and DNA polymerase ε (Pol ε) are replicative DNA polymerases at the replication fork. Both enzymes are stimulated by PCNA, although to different levels. To understand why and to explore the interaction with PCNA, we compared Pol δ and Pol ε in physical interactions with PCNA and nucleic acids (with or without RPA), and in functional assays measuring activity and processivity. Using surface plasmon resonance technique, we show that Pol ε has a high affinity for DNA, but a low affinity for PCNA. In contrast, Pol δ has a low affinity for DNA and a high affinity for PCNA. The true processivity of Pol δ and Pol ε was measured for the first time in the presence of RPA, PCNA and RFC on single-stranded DNA. Remarkably, in the presence of PCNA, the processivity of Pol δ and Pol ε on RPA-coated DNA is comparable. Finally, more PCNA molecules were found on the template after it was replicated by Pol ε when compared to Pol δ. We conclude that Pol ε and Pol δ exhibit comparable processivity, but are loaded on the primer-end via different mechanisms.     

Contrasting Taxonomic and Phylogenetic Diversity Responses to Forest Modifications: Comparisons of Taxa and Successive Plant Life Stages in South African Scarp Forest

The degradation of natural forests to modified forests threatens subtropical and tropical biodiversity worldwide. Yet, species responses to forest modification vary considerably. Furthermore, effects of forest modification can differ, whether with respect to diversity components (taxonomic or phylogenetic) or to local (α-diversity) and regional (β-diversity) spatial scales. This real-world complexity has so far hampered our understanding of subtropical and tropical biodiversity patterns in human-modified forest landscapes. In a subtropical South African forest landscape, we studied the responses of three successive plant life stages (adult trees, saplings, seedlings) and of birds to five different types of forest modification distinguished by the degree of within-forest disturbance and forest loss. Responses of the two taxa differed markedly. Thus, the taxonomic α-diversity of birds was negatively correlated with the diversity of all plant life stages and, contrary to plant diversity, increased with forest disturbance. Conversely, forest disturbance reduced the phylogenetic α-diversity of all plant life stages but not that of birds. Forest loss neither affected taxonomic nor phylogenetic diversity of any taxon. On the regional scale, taxonomic but not phylogenetic β-diversity of both taxa was well predicted by variation in forest disturbance and forest loss. In contrast to adult trees, the phylogenetic diversity of saplings and seedlings showed signs of contemporary environmental filtering. In conclusion, forest modification in this subtropical landscape strongly shaped both local and regional biodiversity but with contrasting outcomes. Phylogenetic diversity of plants may be more threatened than that of mobile species such as birds. The reduced phylogenetic diversity of saplings and seedlings suggests losses in biodiversity that are not visible in adult trees, potentially indicating time-lags and contemporary shifts in forest regeneration. The different responses of taxonomic and phylogenetic diversity to forest modifications imply that biodiversity conservation in this subtropical landscape requires the preservation of natural and modified forests.     

Impact of Logging and Forest Conversion to Oil Palm Plantations on Soil Bacterial Communities in Borneo

Tropical forests are being rapidly altered by logging and cleared for agriculture. Understanding the effects of these land use changes on soil bacteria, which constitute a large proportion of total biodiversity and perform important ecosystem functions, is a major conservation frontier. Here we studied the effects of logging history and forest conversion to oil palm plantations in Sabah, Borneo, on the soil bacterial community. We used paired-end Illumina sequencing of the 16S rRNA gene, V3 region, to compare the bacterial communities in primary, once-logged, and twice-logged forest and land converted to oil palm plantations. Bacteria were grouped into operational taxonomic units (OTUs) at the 97% similarity level, and OTU richness and local-scale α-diversity showed no difference between the various forest types and oil palm plantations. Focusing on the turnover of bacteria across space, true β-diversity was higher in oil palm plantation soil than in forest soil, whereas community dissimilarity-based metrics of β-diversity were only marginally different between habitats, suggesting that at large scales, oil palm plantation soil could have higher overall γ-diversity than forest soil, driven by a slightly more heterogeneous community across space. Clearance of primary and logged forest for oil palm plantations did, however, significantly impact the composition of soil bacterial communities, reflecting in part the loss of some forest bacteria, whereas primary and logged forests did not differ in composition. Overall, our results suggest that the soil bacteria of tropical forest are to some extent resilient or resistant to logging but that the impacts of forest conversion to oil palm plantations are more severe.