Scales of variation in zooplankton communities and monitoring for species of concern in southcentral Alaska

During the last decade, sow mortality due to pelvic organ prolapse (POP) has increased. To better understand the biology associated with POP, sows were phenotypically assessed and assigned a perineal score (PS) based on presumed POP risk and categorized as PS1 (low), PS2 (moderate), or PS3 (high). The study objective was to identify changes in sow vaginal microbiota that may be associated with POP. The hypothesis is that vaginal microbiota differs between sows with variable risk for POP, and changes in microbiota during late gestation exist between sows with differing risk. Of the 2864 sows scored during gestation week 15, 1.0, 2.7, and 23.4% of PS1, PS2, and PS3 sows, respectively, subsequently experienced POP. Vaginal swabs subjected to 16S rRNA gene sequencing revealed differences in community composition (Bray–Curtis; P < 0.05) and individual operational taxonomic unit (OTU) comparisons between vaginal microbiota of PS1 and PS3 sows at gestation week 15. Further, differences (P < 0.05) in community composition and OTUs (Q < 0.05) were observed in PS3 sows that either did or did not subsequently experience POP. Differences in community structure (alpha diversity measurements; P < 0.05), composition (P < 0.05), and OTUs (Q < 0.05) were observed in gestation week 12 sows scored PS1 compared to week 15 sows scored PS1 or PS3, suggesting that sow vaginal microbiota shifts during late gestation differently as POP risk changes. Collectively, these data demonstrate that sows with greater POP risk have unique vaginal microflora, for which a better understanding could aid in the development of mitigation strategies.

The mature meadows (MMs) and the swamp meadows (SMs) are the two most important ecosystems in the eastern Tibetan Plateau, China. Besides their substantial differences in terms of soil water conditions and thereby the soil oxygen and nutrients, however, little is known about the differences in community composition, structure, traits and productivity between these two meadows. We particularly ask whether light availability mediated by physical structure heterogeneity is a key determinant of the difference in community composition and productivity between these two meadows. We examined the community structure, composition, aboveground net primary productivity (ANPP), light availability in understory and the community-weighted means (CWMs) for leaf morphological and physiological traits in 12 random plots (5 m × 5 m) for each of the studied habitats. The results showed that plant community in the MM had higher variation in both vertical and horizontal structure and thus had more light availability in the understory. The MM had higher species richness and greater ANPP than the SM. The CWMs of leaf morphological and physiological traits for species in the MM featured a fast-growing strategy (i.e. higher height, leaf area and net photosynthesis rate and lower nitrogen:phosphorus ratio), in contrast to those in the SM. We also found that there were significant correlations between the CWM of traits and the ANPP, indicating that some key traits in these habitats have linked to community productivity. Our study also suggests that the heterogeneity in the community structure, which affects light availability in the understory, may play an important role in determining the community composition and productivity. In conclusion, our study revealed significant differences in community structure, composition and traits between the MM and the SM, and the light availability that related closely to community structure is the key factor to determine the composition and productivity of the community of these two habitats.

We investigated the communities of woody plants, ground-dwelling insects, soil bacteria, and soil fungi in both karst and non-karst forests within the Yachang Orchids Natural Reserve, Guangxi, to explore the role of plant communities, stand structure, soil and litter properties in driving the differences in biological community composition. The results revealed that species richness, Shannon index, and Simpson index of plants were significantly higher in karst forest than non-karst forest. There were no significant differences in the species richness or Shannon index of ground-dwelling insects, bacteria, and fungi between the two forest types. However, the Simpson index for ground-dwelling insects and bacteria was significantly lower in karst forest, while the Simpson index for fungi was significantly higher. Community composition of the four biological groups differed significantly between karst and non-karst forests. The difference in plant community composition was primarily driven by soil pH (explaining 24.0% of the variation) and total soil carbon content (19.8%), with most plant species contributing to the dissimilarity. The difference in community composition of ground-dwelling insects was mainly driven by plant community composition (30.3%), understory tree density (13.8%), litter total phosphorus content (29.9%), and soil temperature (7.1%). The dissimilarity in ground-dwelling insect community was largely attributed to the differences in the abundances of Nitidulidae, Blattellidae, Gryllidae, Scarabaeidae, and Pycnoscelidae. The difference in bacteria community composition was primarily driven by soil temperature (39.5%) and pH (10.3%), with an unclassified family 1 of Acidobacteria and Pyrinomonadaceae being the key family contributing to the dissimilarity. The difference in fungal community composition was mainly influenced by plant community composition (21.2%), soil temperature (7.6%), and litter total phosphorus content (7.2%), with Russulaceae being the key family contributing to the dissimilarity. Our results suggested that the alkaline soils in karst forests support higher plant diversity, which offsets the negative effects of exposed rock and low soil temperature, thereby maintaining the diversity of other biological groups.

The impact of the occurrence of the non-indigenous species (NIS) Acartia tonsa, Oithona davisae, and Pseudodiaptomus marinus and of the range-expanding copepods Acartia bifilosa and Calanipeda aquaedulcis on the structure and diversity of zooplankton communities was analyzed using 18 years (1998–2015) time series from the contrasting estuaries of Bilbao and Urdaibai (Basque coast, Bay of Biscay). Changes in the structure of communities were assessed by using multivariate analyses of taxa abundances and changes in diversity by using descriptors of alpha, beta, and gamma diversity. The most evident changes occurred at the upper reaches of the estuary of Bilbao, where an abundant and less diverse brackish community, dominated by the NIS, A. tonsa and O. davisae, succeeded a low abundance and more diverse community of neritic origin. The later establishment of C. aquaedulcis was linked to further changes in the structure of the community and a progressive increase in diversity. The seasonal pattern of diversity at the inner estuary and the beta diversity in the estuary were also significantly affected by the arrival of the NIS and C. aquaedulcis. In contrast, the original low diversity brackish community of the estuary of Urdaibai, clearly dominated by A. bifilosa, was far less affected by the arrival of the same copepod NIS, and A. bifilosa remained as the species best related to the changes in zooplankton structure and diversity in the brackish habitats of the estuary.

Many investigations of anthropogenic and natural impacts in ecological systems attempt to detect differences in ecological variables or community composition. Frequently, ordination procedures such as principal components analysis (PCA) or canonical correspondence analysis (CCA) are used to simplify such complex data sets into a set of primary factors that express the variation across the original variables. Scatterplots of the first and second principal components are then used to visually inspect for differences in community composition between treatment groups. We present a multidimensional extension of analysis of variance based on an analysis of distance (ANODIS) that can be used to formally test for differences in community composition using 1, 2, or more dimensions of a PCA or CCA of the original sample observations. The statistical tests of significance are based on F-statistics adapted for the analysis of this multidimensional data. Because the analysis is parametric, power and sample size calculations useful in the design of field studies can be readily computed. The use of ANODIS is illustrated using bivariate PCA scatterplots from three published studies. Statistical power calculations using the noncentral F-distribution are illustrated.

Epifaunal invertebrates play an important role in seagrass systems, both by grazing epiphytic algae from seagrass blades and by acting as a major food source for higher trophic levels. However, while many studies have described epifaunal community properties at small spatial scales (1–10 m2) and across very large gradients (from continental coastlines to the entire globe), few have examined regional-scale (100–1000 km2) patterns or, more importantly, disentangled the drivers of these patterns. Here, we synoptically sampled the epifaunal invertebrates of 16 sites dominated by eelgrass (Zostera marina) across the lower Chesapeake Bay estuary to describe differences in epifaunal community abundance, biomass, richness, and composition. We then used complementary spatial and environmental data to identify potential drivers of these patterns. We found no significant associations between any variable and epifaunal abundance or biomass, but differences in epifaunal species richness correlated most strongly with water temperature, and differences in community composition were best explained by seagrass cover and the biomass of algal resources. Further exploration revealed the relationship between cover and community structure was driven by three specific species of peracarid crustaceans. Furthermore, when only species with direct development were included in the analysis, geographic distance, rather than seagrass cover, became a significant predictor of community composition, suggesting that species with particular traits (i.e., direct developers) are more likely to be found closer together in space.

The far north of Ontario, Canada, is a region that is very vulnerable to future change due to climate warming and resource extraction. Despite its vast size (~ 450,000 km2) and large numbers of lakes (> 700,000), there has been very little study of aquatic ecosystems in this remote area. To address this lack of limnological data, forty-one northern Ontario lakes spanning two physiographic regions, the Hudson Bay Lowlands and the Canadian Shield, were sampled during 2012 for crustacean zooplankton and water chemistry. These sub-Arctic lakes support diverse crustacean plankton communities with species richness similar to the richness of lakes in central and northeastern Ontario. While some of the species collected appear to be at the northern limit of their distributions, most relatively common Ontario species occurred throughout the 2012 study area. The physico-chemical characteristics showing relationships with species richness and relative abundances were variables associated with lake morphometry, ionic strength and nutrient status. There were differences in community richness and composition between Lowlands and Shield lakes; however, these differences do not seem attributable to biogeographical influences on species occurrences. Rather, the lower species richness and differences in community composition in Lowlands lakes relative to Shield lakes appear to be largely related to lake morphometry. The shallower and generally smaller Lowlands lakes provide much less habitat diversity, i.e. niche space, than the larger, deeper Shield lakes, leading to simpler communities.

Pastures are an important part of crop and food systems in cold climates. Understanding how fertilization and plant species affect soil bacterial community diversity and composition is the key for understanding the role of soil bacteria in sustainable agriculture. To study the response of soil bacteria to different fertilization and cropping managements, a 3-year (2013–2015) field study was established. In the split-plot design, fertilizer treatment (unfertilized control, organic fertilizer, and synthetic fertilizer) was the main plot factor, and plant treatment [clear fallow, red clover (Trifolium pratense), timothy (Phleum pratense), and a mixture of red clover and timothy] was the sub-plot factor. Soil bacterial community diversity and composition, soil properties, and crop growth were investigated through two growing seasons in 2014 and 2015, with different nitrogen input levels. The community diversity measures (richness, Shannon diversity, and Shannon evenness) and composition changed over time (P < 0.05) and at different time scales. The community diversity was lower in 2014 than in 2015. The temporal differences were greater than the differences between treatments. The overall correlations of Shannon diversity to soil pH, NO, NH, and surplus nitrogen were positive and that of bacterial richness to crop dry matter yield was negative (P < 0.05). The major differences in diversity and community composition were found between fallow and planted treatments and between organic and synthetic fertilizer treatments. The differences between the planted plots were restricted to individual operational taxonomic units (OTUs). Soil moisture, total carbon content, and total nitrogen content correlated consistently with the community composition (P < 0.05). Compared to the unfertilized control, the nitrogen fertilizer loading enhanced the temporal change of community composition in pure timothy and in the mixture more than that in red clover, which further emphasizes the complexity of interactions between fertilization and cropping treatments on soil bacteria.

Parasitoid assemblages infesting Yponomeuta species in the Netherlands were investigated. Parasitoid species richness and community composition were related to host species, habitat, temporal and spatial variation. Both community structure and species richness did not differ among habitats. There was no significant difference in species richness between years (1994 and 1995) but there was a significant difference in community composition. Community composition and species richness both differed among host species, although this latter result was solely due to the host species Y. evonymellus. There was no significant relationship between community similarity and distance. These results indicate that the parasitoids of the moth genus Yponomeuta in the Netherlands appear to form a spatially stable, but temporally variable community. Most of the variation in community structure was, however, related to the host species. The marked difference in parasitoid species richness and community composition of Y. evonymellus when compared to the other species warrants further study.

ABSTRACTIntroductionTo evaluate the antimicrobial activity and changes in community composition in biofilms treated with two root canal sealers or calcium hydroxide.Material and MethodsForty‐nine extracted bovine dentine cylinders were inoculated with subgingival dental plaque for 2 weeks in a CDC biofilm reactor. Three treatment groups were assigned: AH Plus, BC Sealer, and calcium hydroxide. Propylene glycol inert vehicle (PG) and untreated contaminated samples were used as controls. The infected root canal space was in direct contact with the materials for 7 days under anaerobic incubation. Anaerobic culture (colony forming units, CFU), quantification PCR (qPCR), and next generation sequencing were used to assess the effect of each material. Differences in the number of molecules (qPCR), CFU, and abundances of genera were evaluated using the Kruskal–Wallis test. The Shannon and Chao1 indices were used to measure alpha diversity. Differences in community composition were evaluated using non‐parametric analysis of similarity (ANOSIM).ResultsThe CFU, Shannon, and Chao1 indices revealed significant differences between BC Sealer, AH Plus, and calcium hydroxide groups versus the untreated control group and PG (p < 0.003). Calcium hydroxide and BC Sealer significantly reduced the qPCR values compared to the control group and PG. The biofilm composition (98.5%) was primarily composed of Peptostreptococcus, Streptococcus, Parvimonas, Fusobacterium, Veillonela, Mogibacterium, Lancefieldella, Eubacterium, Slackia, and Prevotella. Significant differences in overall community composition and beta diversity between untreated controls and AH Plus were observed (ANOSIM R = 0.674, p < 0.001). Parvimonas, Streptococcus, Eubacterium, and Lancefieldella were not affected by any of the materials tested.ConclusionCalcium hydroxide and BC Sealer significantly reduced the viability and the total number of DNA copies. AH Plus sealer reduced the bacterial viability but did not affect the DNA concentration. AH Plus significantly alters overall biofilm community composition compared to other groups. None of the materials tested eliminated the multispecies biofilm completely.

Permafrost disturbance (shoreline retrogressive thaw slumping [SRTS]) causes solute-rich terrestrial inputs to Arctic tundra lakes. Eight upland tundra lakes (3 undisturbed [U], 5 disturbed [D]) in the Inuvik region of the Northwest Territories, Canada, were sampled to assess the effects of SRTS on benthic invertebrate community structure, abundance, and whether localized SRTS effects in D lakes could be discriminated by comparing samples taken adjacent to (Da) or further from (Do) the disturbance. Community composition and abundance differed between U and D lakes. Macroinvertebrates were more abundant in areas adjacent to SRTS (Da) than in areas away from SRTS (Do), but community composition did not differ between Da and Do areas. Abundance was >2× greater in D than in U lakes. Ostracoda abundance was 4× greater in D than U lakes and 2× higher in Da than Do areas. Nematoda abundance was ∼10× higher in D than U lakes, whereas Chironomidae abundance was lower in D than U lakes. Bivalvia and Oligochaeta had similar abundance in D and U lakes, and both groups were more abundant in Da than Do areas. Differences in abundance and community composition were related primarily to higher concentrations of Ca2+ in D than U sediments and to higher organic C and N in U than D sediments. Sediment organic C and Mg concentrations, macrophyte biomass, and dissolved organic C concentrations best explained differences in community composition among lake types and areas. Our study adds to our understanding of cascading changes in the foodweb structure and ecological states of freshwater ecosystems caused by climate change in the Arctic.

We investigated the influence of 6 morphometric and geographic factors on the structure and composition of plant communities in 56 temporary freshwater rockpools from 7 pool landscapes in the Maltese Islands. The factors considered were water depth, sediment depth, surface area, shading, distance from the coast, and elevation above sea level. Coverage data for 30 plant taxa in 3 functional forms (aquatic, amphibious, and terrestrial) were collected during one hydrological cycle. The relationships between pool morphometry, pool location, and community composition were tested using multivariate analyses. The contribution of spatial variables to variation in community composition across pools was examined using principal coordinate analysis of neighbour matrices (PCNM). The results suggested that pool morphometry varied both within and across landscapes, reflected in similar differences in community composition. Moreover, 47.6% of the explained community variation in the whole dataset was contributed exclusively by space predictors, suggesting that pool “location” is an important determinant of community composition. The morphometric property that exerted the highest influence on the dominance of a given plant functional form was the pool surface area, with greater surface areas promoting the presence of amphibious species relative to obligate hydrophytes. Conversely, the presence of specific species was mainly controlled by water depth and sediment depth. The most influential predictors of community composition varied across landscape, suggesting that pool location can be an important determinant of community structure and composition, and pool morphometry would favour certain functional forms and species over others.

Forests contribute to numerous ecosystem functions and services and contain a large proportion of terrestrial biodiversity, but they are being negatively impaced by anthropogenic activities. Forests that have never been clear-cut and have old growth characteristics, termed "near-natural," often harbor different and richer species assemblages than managed forests. Alternative management strategies may be able to balance the needs of biodiversity with the demands of forestry, but evaluation efforts are limited by the challenges of measuring biodiversity. Species richness is frequently used as a simple measure of biodiversity, but research indicates that it may not adequately capture community-level changes. Alternatively, trait-based measures of biodiversity may prove to be useful, but research is lacking. In this paper, we use a large dataset that includes 339 obligate saproxylic beetle species collected over a decade in the boreal region throughout southern Norway to: (1) establish if there is a difference in beetle community composition between near-natural and managed forests; and (2) determine which measures of beetle biodiversity best indicate forest naturalness. We arranged the sites in an ordination space and tested for differences in community composition between these forest types. We also tested different measures of biodiversity to determine which were the most predictive of forest naturalness. We found a clear difference in community composition between near-natural and managed forests. Additionally, three measures of biodiversity were most predictive of forest naturalness: proportional abundance of predators, community weighted mean (CWM) of wing length, and CWM of body roundness. The probability that a forest was near-natural increased with the proportional abundance of predators but decreased with CWM wing length and body roundness. Although species richness was higher in near-natural forests, the effect was not significant. Overall, our findings underscore the conservation value of near-natural forests and highlight the potential of several measures of biodiversity for determining forest quality.

Habitat alteration via urbanization has very different effects on even closely related taxa. Most research investigating the ecological effects of urbanization has focused on birds or mammals, resulting in a relatively poor understanding of how the species richness and community composition of invertebrates may change. We quantified differences in species richness of adult odonates (dragonflies and damselflies) at lentic and lotic sites in urban and rural landscapes, and we examined environmental factors that might drive the differences in community composition that we observed. For lotic sites, species richness did not differ between urban versus rural sites for either dragonflies or damselflies. For lentic sites, urban and rural sites contained similar dragonfly species richness, but damselfly species richness was significantly lower at urban sites than at rural sites. Differences in lentic odonate community composition were associated with the amount of urban development within 150 m of each site, mean algal coverage, and distance to the urban center. At lotic sites, water temperature and distance to the urban center were correlated with differences in odonate community composition. The differing responses to urbanization observed in this study were probably a consequence of differences between lentic versus lotic ecosystems and between dragonflies versus damselflies in dispersal capability and habitat specificity. Given that different environmental factors affected these taxa differently in lentic and lotic sites, maintaining the highest level of odonate diversity possible across a landscape will require the use of different management practices for each ecosystem type.

Vascular epiphytes contribute to the structural, compositional, and functional complexity of tropical montane cloud forests because of their high biomass, diversity, and ability to intercept and retain water and nutrients from atmospheric sources. However, human‐caused climate change and forest‐to‐pasture conversion are rapidly altering tropical montane cloud forests. Epiphyte communities may be particularly vulnerable to these changes because of their dependence on direct atmospheric inputs and host trees for survival. In Monteverde, Costa Rica, we measured vascular epiphyte biomass, community composition, and richness at two spatial scales: (1) along an elevation gradient spanning premontane forests to montane cloud forests and (2) within trees along branches from inner to outer crown positions. We also compared epiphyte biomass and distribution at these scales between two different land‐cover types, comparing trees in closed canopy forest to isolated trees in pastures. An ordination of epiphyte communities at the level of trees grouped forested sites above versus below the cloud base, and separated forest versus pasture trees. Species richness increased with increasing elevation and decreased from inner to outer branch positions. Although richness did not differ between land‐cover types, there were significant differences in community composition. The variability in epiphyte community organization between the two spatial scales and between land‐cover types underscores the potential complexity of epiphyte responses to climate and land‐cover changes.Abstract in Spanish is available with online material.