Community Similarity Measures Research Articles

Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades

BackgroundMicroorganisms such as coliform-forming bacteria are commonly used to assess freshwater quality for drinking and recreational use. However, such organisms do not exist in isolation; they exist within the context of dynamic, interactive microbial communities which vary through space and time. Elucidating spatiotemporal microbial dynamics is imperative for discriminating robust community changes from ephemeral ecological trends, and for improving our overall understanding of the relationship between microbial communities and ecosystem health. We conducted a seven-year (2013–2019) microbial time-series investigation in the Chicago Area Waterways (CAWS): an urban river system which, in 2016, experienced substantial upgrades to disinfection processes at two wastewater reclamation plants (WRPs) that discharge into the CAWS and improved stormwater capture, to improve river water quality and reduce flooding. Using culture-independent and culture-dependent approaches, we compared CAWS microbial ecology before and after the intervention.ResultsExaminations of time-resolved beta distances between WRP-adjacent sites showed that community similarity measures were often consistent with the spatial orientation of site locations to one another and to the WRP outfalls. Fecal coliform results suggested that upgrades reduced coliform-associated bacteria in the effluent and the downstream river community. However, examinations of whole community changes through time suggest that the upgrades did little to affect overall riverine community dynamics, which instead were overwhelmingly driven by yearly patterns consistent with seasonality.ConclusionsThis study presents a systematic effort to combine 16S rRNA gene amplicon sequencing with traditional culture-based methods to evaluate the influence of treatment innovations and systems upgrades on the microbiome of the Chicago Area Waterway System, representing the longest and most comprehensive characterization of the microbiome of an urban waterway yet attempted. We found that the systems upgrades were successful in improving specific water quality measures immediately downstream of wastewater outflows. Additionally, we found that the implementation of the water quality improvement measures to the river system did not disrupt the overall dynamics of the downstream microbial community, which remained heavily influenced by seasonal trends. Such results emphasize the dynamic nature of microbiomes in open environmental systems such as the CAWS, but also suggest that the seasonal oscillations remain consistent even when perturbed.

Invasive species and biotic homogenization in temperate aquatic plant communities

AbstractAimBiotic homogenization (BH), a reduction in the distinctness of species composition between geographically separated ecological communities in a region, is an important but underappreciated potential consequence of biological invasions. While BH theory has always considered invasions, it has generally been in a relatively narrow context that the cosmopolitan nature of invasive species increases BH because of their shared presence across many locations. We sought to evaluate this component of BH as well as broader effects of invasive species on BH through changes in native communities, including overall reductions in species richness or shifts in species composition.LocationMinnesota, USA.Time period2002–2014.Major taxa studiedAquatic macrophytes, including both vascular plants and attached macroalgae.MethodsWe used surveys of aquatic macrophyte communities from 1,102 shallow lakes in Minnesota, USA (including 248 lakes with repeated surveys) to evaluate relationships between invasion, native species and BH.ResultsWe found that the presence of invasive species was associated with BH and that this pattern was reflected in both the total community (i.e., with invasive species included) and in the composition of the native species community alone. We found that invaded lakes were more compositionally similar to each other than uninvaded lakes, but that both groups were becoming more similar over time—despite neither group exhibiting declines in species richness. This pattern was largely driven by shifts in the native community itself, with common species becoming more widespread and rare species becoming rarer.Main conclusionsInvasive species increase measures of community similarity through their own presence in multiple locations, and also by influencing the composition of native species. These patterns have important implications for conservation and management and suggest that BH should be considered more widely in evaluating the impacts of biological invasions and developing response strategies.

Does the maternal vaginal microbiota play a role in seeding the microbiota of neonatal gut and nose?

The acquisition and early maturation of infant microbiota is not well understood despite its likely influence on later health. We investigated the contribution of the maternal microbiota to the microbiota of infant gut and nose in the context of mode of delivery and feeding. Using 16S rRNA sequencing and specific qPCR, we profiled microbiota of 42 mother-infant pairs from the GUSTO birth cohort, at body sites including maternal vagina, rectum and skin; and infant stool and nose. In our study, overlap between maternal vaginal microbiota and infant faecal microbiota was minimal, while the similarity between maternal rectal microbiota and infant microbiota was more pronounced. However, an infant's nasal and gut microbiota were no more similar to that of its own mother, than to that of unrelated mothers. These findings were independent of delivery mode. We conclude that the transfer of maternal vaginal microbes play a minor role in seeding infant stool microbiota. Transfer of maternal rectal microbiota could play a larger role in seeding infant stool microbiota, but approaches other than the generally used analyses of community similarity measures are likely to be needed to quantify bacterial transmission. We confirmed the clear difference between microbiota of infants born by Caesarean section compared to vaginally delivered infants and the impact of feeding mode on infant gut microbiota. Only vaginally delivered, fully breastfed infants had gut microbiota dominated by Bifidobacteria. Our data suggest that reduced transfer of maternal vaginal microbial is not the main mechanism underlying the differential infant microbiota composition associated with Caesarean delivery. The sources of a large proportion of infant microbiota could not be identified in maternal microbiota, and the sources of seeding of infant gut and nasal microbiota remain to be elucidated.

Fish Passage Through Three Types of Structures in Diked Coastal Lake Erie Wetlands

AbstractOver 40% of Great Lakes fishes are wetland dependent, and more than 70% benefit from wetlands periodically. As such, restoration and rehabilitation of Great Lakes coastal wetlands have increased dramatically. This necessitates a balance among varied management objectives, including fish passage. The presence of water control structures commonly found on diked wetlands can limit fish passage if not open all the time. We sampled three diked Lake Erie coastal wetlands to assess how different structures affected fish passage. Water control structures included a pool‐and‐weir fish ladder, swing gates, and an open culvert. Fyke nets were set five to seven times at each site between April and October 2015. One net was set outside of the wetland, a short distance away from the passage structure, and the other was set inside the wetland, with the net wings enclosing the opening of the structure. Catches were compared for catch rate, three measures of community similarity, and the wetland fish index (WFI). Fish communities on either side of the fish ladder site had low community similarities that were lower than those of the culvert site and similar to those of the swing gate site, suggesting that the fish ladder did not provide fish passage as hoped. Of the three wetlands, catches from inside the wetland with the culvert had a WFI that was most similar to those of wetlands connected to Lake Erie hydrology. Overall, the culvert provided the most opportunity for fish movement into the wetland. However, unlike the other structures, it did not provide a means for precisely managing wetland water levels.Received September 30, 3016; accepted January 25, 2017 Published online April 4, 2017

Identifying Temperature Thresholds Associated with Fish Community Changes in British Columbia, Canada, to Support Identification of Temperature Sensitive Streams

AbstractWe collected fish samples and measured physical habitat characteristics, including summer stream temperatures, at 156 sites in 50 tributary streams in two sampling areas (Upper Fraser and Thompson Rivers) in British Columbia, Canada. Additional watershed characteristics were derived from GIS coverages of watershed, hydrological and climatic variables. Maximum weekly average temperature (MWAT), computed as an index of summer thermal regime, ranged from 10 to 23 °C. High values of MWAT were associated with large, warm, low relief watersheds with a high lake influence. Measures of community similarity suggested that the fish community changed most rapidly through a lower transition zone at an MWAT of about 12 °C and an upper transition zone at an MWAT of about 19 °C. These results were confirmed using existing fisheries inventory data combined with predictions of MWAT from a landscape‐scale regression model for the Thompson River watershed. For headwater sites in the Chilcotin River watershed (which drains into the middle Fraser River), the relative dominance of bull trout versus rainbow trout (based on inventory data) decreased with increasing predicted MWAT although the distinction was not as clear as for the Thompson River sites. The fish communities in these watersheds can be characterized in terms of very cold water (bull trout and some cold water species), cold water (salmonids and sculpins) and cool water (minnows and some cold water salmonids). The two transition zones (ca 12 and 19 °C) can be used to identify thresholds where small changes in stream temperature can be expected to lead to large changes in fish communities. Such clear, quantifiable thresholds are critical components of a management strategy designed to identify and protect vulnerable fish communities in streams where poor land use practices, alone or in combination with climatic change, can lead to changes in stream temperatures. Copyright © 2015 John Wiley & Sons, Ltd.

Hierarchical Agglomeration Community Detection Algorithm via Community Similarity Measures

Community detection is an important method for analyzing the community structure of real-world networks. Most of the hierarchical agglomeration community detection algorithms are the variations of NM algorithm. In this contribution, we present a new hierarchical agglomeration community detection algorithm, called Community Merging via Community Similarity Measures (CMCSM). The proposed algorithm encompasses three components. It first repeatedly joins communities by using single-node community measure and combination rule. Then it adjusts a few nodes by SHARC which is an advanced label propagation algorithm. Finally, it merges communities by using community similarity measure. Four of most important features of CMCSM are that (1) it requires only a single parameter which is the number of community count, (2) it can prevent single-node communities and monster communities from being created, (3) it is well suited for a wide range of networks and (4) its computation is not expensive. The algorithm CMCSM is demonstrated with real-world and artificial networks, the experiment shows that CMCSM has a more efficient and accurate result of community detection compared with some hierarchical algorithms recently proposed. DOI: http://dx.doi.org/10.11591/telkomnika.v10i6.1430 Full Text: PDF

Measuring Community Similarity with Phylogenetic Networks

Environmental drivers of biodiversity can be identified by relating patterns of community similarity to ecological factors. Community variation has traditionally been assessed by considering changes in species composition and more recently by incorporating phylogenetic information to account for the relative similarity of taxa. Here, we describe how an important class of measures including Bray-Curtis, Canberra, and UniFrac can be extended to allow community variation to be computed on a phylogenetic network. We focus on phylogenetic split systems, networks that are produced by the widely used median network and neighbor-net methods, which can represent incongruence in the evolutionary history of a set of taxa. Calculating β diversity over a split system provides a measure of community similarity averaged over uncertainty or conflict in the available phylogenetic signal. Our freely available software, Network Diversity, provides 11 qualitative (presence-absence, unweighted) and 14 quantitative (weighted) network-based measures of community similarity that model different aspects of community richness and evenness. We demonstrate the broad applicability of network-based diversity approaches by applying them to three distinct data sets: pneumococcal isolates from distinct geographic regions, human mitochondrial DNA data from the Indonesian island of Nias, and proteorhodopsin sequences from the Sargasso and Mediterranean Seas. Our results show that major expected patterns of variation for these data sets are recovered using network-based measures, which indicates that these patterns are robust to phylogenetic uncertainty and conflict. Nonetheless, network-based measures of community similarity can differ substantially from measures ignoring phylogenetic relationships or from tree-based measures when incongruent signals are present in the underlying data. Network-based measures provide a methodology for assessing the robustness of β-diversity results in light of incongruent phylogenetic signal and allow β diversity to be calculated over widely used network structures such as median networks.

Range size variation, nestedness and species turnover of orchid species along an altitudinal gradient on Réunion Island: Implications for conservation

Tropical oceanic islands contribute disproportionably for their area to global biodiversity and this is especially true for islands with strong altitudinal gradients. On these islands, species richness and composition usually change with altitude, but the way in which they do may vary from one system to the next. Better insights in how species richness and composition are related may have far-reaching conservation implications. At the one extreme, species composition of a species-poor site may be completely different from that of the most species-rich site. In this case, conservation of the species-poor site should be encouraged as it contains species that are not to be found elsewhere. At the other extreme, species composition of the species-poor sites may be a subset of the species-rich sites (i.e. nestedness or nested subsets). Focus on the most species-rich site may be sufficient to effectively conserve a maximum of species. In this study, we determined changes in species richness and composition of orchid species along an altitudinal gradient spanning more than 2500 m on Réunion Island (Mascarenes). A formal nestedness analysis was performed to investigate whether species-poor sites were a subset of species-rich sites and whether this was related to altitude. Differences in species composition along the altitudinal gradient were determined using two different measures of community similarity. The species-by-sites matrix was significantly nested when sorted by species richness, but not when sorted by altitude. Mean similarity indices were low at both low and high altitude sites, indicating significant turnover of orchid species. Our results suggest that reserve selection should be based on two basic principles: (1) maximize the number of vegetation zones in which reserves are to be placed and (2) within each zone, select the sites with the highest species richness. Given that at present only two nature reserves are present on the island, our results further suggest that they are not sufficient to effectively conserve the extremely high orchid diversity on Réunion Island.

Insect Biodiversity on Plant Hybrids Within the Hawaiian Silversword Alliance (Asteraceae: Heliantheae-Madiinae)

Patterns of arthropod richness and diversity were studied across six hybrid zones within the silversword alliance (Asteraceae: Heliantheae-Madiinae), an adaptive radiation of endemic Hawaiian plants. Hybrid zones spanned a range of parental plant relatedness from those in which parental types were phenotypically and genetically similar to those in which parental types were different both phenotypically and genetically. This system of hybrid zones is uniquely suited for distinguishing among alternative hypotheses that account for biodiversity of herbivores in plant hybrid zones. In the six hybrid zones studied, arthropod family-level diversity was as high or higher on hybrid plants compared with parental plants. Family-level richness was as high or higher on hybrids plants in four cases and lower on hybrids in two cases. Generally, results were consistent with hypotheses that predict either a breakdown in insect defenses in hybrid plants or an additive increase in host recognition cues in hybrids. Hypotheses that predict an increase in hybrid resistance to herbivory were supported in two cases. Measures of community similarity suggest insect communities are more similar to each other on hybrid-parent pairs than are communities on parent-parent pairs and that insect communities across interspecific hybrid zones are more similar than communities across intergeneric hybrid zones. In four zones, hybrids supported unique arthropod taxa. Because a greater or equal diversity of arthropods is found on hybrids than on parental plant taxa and because hybrid plants may represent unique environments to insects, plant hybrid zones are important targets for conserving Hawaii's native biota.

Beyond Species Richness: Community Similarity as a Measure of Cross‐Taxon Congruence for Coarse‐Filter Conservation

Abstract: The use of a surrogate taxon in conservation planning has become questionable because recent evidence suggests that the correlation of species richness between pairs of taxa is highly variable both taxonomically and geographically. Species richness is only one measure of species diversity, however, and recent studies suggest that investigations of cross‐taxon congruence should consider a broader range of assessment techniques. The cross‐taxon congruence of community similarity between sites among taxa has rarely been examined and may be the most relevant measure of species diversity in the context of coarse‐filter conservation strategies. We examined cross‐taxon congruence patterns of species richness and community similarity (Bray‐Curtis similarity) among birds, butterflies, and vascular plants in montane meadow habitats in the Greater Yellowstone Ecosystem. Although patterns of species richness (Spearman rank correlation) varied between taxa, we consistently found a positive correlation in community similarity (Mantel test) between all pair‐wise comparisons of the three taxa (e.g., sites with similar bird communities also had similar butterfly communities). We suggest that the success of a surrogate taxon depends on the technique used to assess surrogacy and the specific approach to conservation planning. In the context of coarse‐filter conservation, measures of community similarity may be more appropriate than measures of species richness. Furthermore, the cross‐taxon congruency of community similarity in our study suggests that coarse‐filter conservation may be tenable in montane meadow communities.

Tree and shrub diversity and abundance in fragmented littoral forest of southeastern Madagascar

In the coastal littoral forest of extreme southeastern Madagascar, we studied tree diameter at breast height (DBH) $ 10 cm in 20, 50 3 50 m plots in each of four forest fragments, and understory woody vegetation (DBH , 10 cm, $1 m tall) in 60, 10 3 10 m plots in three of the fragments. One forest fragment was located in the highly degraded Lokaro region, and three in the nearby Sainte-Luce forest. A total of 3476 trees, representing 169 species in 55 families, were recorded in the 50 3 50 m plots, and 10 282 understory stems, representing 195 species in 54 families, were found in the 10 3 10 m plots. For each tree, DBH was recorded. Mean tree diameter and patterns of tree size class distribution did not differ among the four forest fragments. However, the fragments differed significantly in both tree and understory stem densities, species richness and diversity values, and family richness values, with the Lokaro fragment having the lowest values for all measures. Furthermore, floristic patterns, family importance values, and community similarity measures revealed that the species composition at the Lokaro fragment was very different from the Sainte-Luce fragments. Anthropogenic disturbance appears most pronounced in the isolated Lokaro forest, where biotic resources are limited to this single fragment.

Comparisons of benthic communities adjacent to riparian native eucalypt and introduced willow vegetation

1. Willows, Salix spp., have been widely introduced as a riparian species in temperate Australia and New Zealand. The present study was a broad‐scale observational survey to document the differences between reaches of river lined with willows and native vegetation in the community structure of benthic invertebrates and the resources which these plants use.2. Nine rivers in south‐eastern Tasmania were examined on three occasions in autumn, spring and summer. Taxa were identified to family level, with the exception of Oligochaeta and Acarina, and benthic organic matter (CPOM and FPOM) and epilithic biomass were measured for each reach.3. Taxon diversity and evenness were lower in willowed reaches in autumn, and total macroinvertebrate density and number of taxa were lowest in willowed reaches in summer. No differences in the fauna between willowed and native reaches were observed in spring. Measures of community similarity of the fauna in willowed and native reaches were significantly different in autumn and summer, but not in spring.4. The taxa responsible for the significant differences seemed to be responding to differences in food availability and habitat quality in reaches of each vegetation type. Organic matter standing stock was higher in willowed reaches in autumn although the influence of these litter inputs on the fauna were not marked. Epilithon biomass was highest in autumn and spring in willowed reaches when shading in these reaches was least.5. The most marked differences between willowed and native reaches were during summer low flows, when the instream fauna appeared to be responding to changes to shading, water quality and the quality of the habitat.