Comparison Of Community Structure Research Articles

Oyster reefs as habitat for aquatic macrofauna in a Gulf of Mexico estuary: biotic complexity at spatial, ecological, and demographic scales

Oysters are important marine foundation species across the world, particularly in estuaries of the Gulf of Mexico. One important function of oysters in estuaries is the provision of 3-dimensional habitat that is used by a wide range of species. In this study, the biotic diversity of mid-bay intertidal oyster reefs found in a Gulf of Mexico estuary was examined at nested ecological and demographic scales. Fishery-independent data collections made in East Matagorda Bay, Texas, USA, were used to compare community structure and diversity at mid-bay reefs to undifferentiated shoreline habitats. Despite similar diversity metrics, there were differences in community structure that were driven by differences in spatial habitat use by several common species. Below the community scale, demographic differences in spotted seatrout Cynoscion nebulosus habitat use were observed, with smaller and younger individuals found along reefs, and larger and older individuals found along shorelines. This finding was more pronounced for male spotted seatrout in the spring. The observed spatial habitat use patterns at nested ecological scales (community, inter-species, intra-species) highlight the importance of oyster reefs for maintaining diversity in Gulf of Mexico estuaries, and more broadly support the notion that heterogeneity in localized habitats drives biotic diversity at the estuary scale. Conservation of oyster reefs as critical habitat should be considered along with conservation of oysters themselves when balancing the ecological value of oysters against the commercial value of oyster fisheries.

Assessing phytoplankton community composition in the Atlantic Ocean from in situ and satellite observations

The Atlantic Meridional Transect (AMT) program (www.amt-uk.org) provides the perfect opportunity to observe the phytoplankton community size structure over a long latitudinal transect 50oN to 50oS, thereby covering the most important latitude-related basin-scale environmental gradients of the Atlantic Ocean. This work presents cell abundance data of phytoplankton taxa recently collected during cruises AMT28 and 29 (in 2018 and 2019, respectively) using flow cytometer and microscope observations, as well as the pigment composition of the community, to assess the abundance and spatial distribution of taxonomic groups across the Atlantic. The community size structure showed a clear consistency between cruises at large spatial scale, with a dominance of picoplanktonic Cyanobacteria in oceanic gyres, an increase in all groups in the equatorial upwelling region, and high biomass of microplankton size class at higher latitudes. Phytoplankton carbon biomass for oceanographic provinces, ranged from median values of 10 to 47 mg Carbon m-3, for the oligotrophic gyres, and South Atlantic (45°S-50oS), respectively. Satellite images of total chlorophyll a (as a proxy for phytoplankton biomass) as well as the relative contribution of the three phytoplankton size classes were produced for both cruises, and despite the small number of matchups, statistically agreed well with in situ size classes estimated as carbon biomass, constituting the first attempt in the literature to match satellite size classes with in situ data derived from cell abundance. The comparison of community structure between recent cruises (2019, 2018, 2015) and earlier ones (1995-1998) indicates a decrease in the number of diatom-bloom forming species, and an increase in Dinoflagellates, whereas nitrogen-fixing Trichodesmium abundance in tropical Atlantic remains constant. Within the recent period, a relative increase in the median values of picoplankton fraction was seen in SATL region, counterbalanced by a decrease in both nano- and microplankton fractions. Additionally, this study includes a database of species identified by microscopy, which had been interrupted for 20 years, providing a basis for long-term series of phytoplankton species.

Temporal Variations in the Gut Microbiota of the Globally Endangered Sichuan Partridge (Arborophila rufipectus): Implications for Adaptation to Seasonal Dietary Change and Conservation.

Host-associated microbiotas are known to influence host health by aiding digestion, metabolism, nutrition, physiology, immune function, and pathogen resistance. Although an increasing number of studies have investigated the avian microbiome, there is a lack of research on the gut microbiotas of wild birds, especially endangered pheasants. Owing to the difficulty of characterizing the dynamics of dietary composition, especially in omnivores, how the gut microbiotas of birds respond to seasonal dietary changes remains poorly understood. The Sichuan partridge (Arborophila rufipectus) is an endangered pheasant species with a small population endemic to the mountains of southwest China. Here, 16S rRNA sequencing and Tax4Fun were used to characterize and compare community structure and functions of the gut microbiota in the Sichuan partridges across three critical periods of their annual life cycle (breeding, postbreeding wandering, and overwintering). We found that the microbial communities were dominated by Firmicutes, Proteobacteria, Actinobacteria, and Cyanobacteria throughout the year. Diversity of the gut microbiotas was highest during postbreeding wandering and lowest during the overwintering periods. Seasonal dietary changes and reassembly of the gut microbial community occurred consistently. Composition, diversity, and functions of the gut microbiota exhibited diet-associated variations, which might facilitate host adaptation to diverse diets in response to environmental shifts. Moreover, 28 potential pathogenic genera were detected, and their composition differed significantly between the three periods. Investigation of the wild bird gut microbiota dynamics has enhanced our understanding of diet-microbiota associations over the annual life cycle of birds, aiding in the integrative conservation of this endangered bird. IMPORTANCE Characterizing the gut microbiotas of wild birds across seasons will shed light on their annual life cycle. Due to sampling difficulties and the lack of detailed dietary information, studies on how the gut microbiota adapts to seasonal dietary changes of wild birds are scarce. Based on more detailed dietary composition, we found a seasonal reshaping pattern of the gut microbiota of Sichuan partridges corresponding to their seasonal dietary changes. The variation in diet and gut microbiota potentially facilitated the diversity of dietary niches of this endangered pheasant, revealing a seasonal diet-microbiota association across the three periods of the annual cycle. In addition, identifying a variety of potentially pathogenic bacterial genera aids in managing the health and improving survival of Sichuan partridges. Incorporation of microbiome research in the conservation of endangered species contributes to our comprehensive understanding the diet-host-microbiota relationship in wild birds and refinement of conservation practices.

Bee–plant interaction and community response along an urbanization gradient

Abstract Elucidating bee response to urbanization is essential to promoting pollinator diversity in cities especially considering such landscapes are projected to expand to support future global populations. To determine how bee community composition and plant–pollinator interactions respond to urbanization, 29 sites representing three urban categories (high, medium and low urbanization) were monitored biweekly from May through early October in Toronto, Canada. Bees were collected passively using pan and blue vane traps as well as actively using aerial nets and vacuums to compare community structure and plant–pollinator networks among urban categories. Functional traits such as dietary breadth, behaviour, nesting substrate and native or non-native status were also examined to determine how landscape influences bee community assemblages. In total, 5477 bees, comprising 26 genera and 164 species, were represented in this study. The urban landscape was largely supportive of species within the family Apidae and Halictidae as well as ground nesting, native and generalist species. Overall, community composition was affected by urban landscape characteristics such as percent tree cover and impervious (i.e. paved and built) surface surrounding sites; however, bee richness and abundance were significantly influenced by plant richness and not by landscape variables. A total of 3267 interactions were observed throughout the study region with characteristics of plant–pollinator networks remaining consistent along the urban gradient with a few floral host plants such as Solidago dominating interactions in certain urban contexts. These results provide important land use and floral host information for targeting pollinator conservation and habitat restoration.

Tackling inconsistencies among freshwater invertebrate trait databases: harmonising across continents and aggregating taxonomic resolution

Abstract Use of invertebrate traits rather than species composition may facilitate large‐scale comparisons of community structure and responses to disturbance in freshwater ecology because the same traits potentially occur everywhere. In recent years, comprehensive invertebrate trait databases have been established at different scales (e.g., regions, continents). The wide availability of invertebrate trait data supports large‐scale studies. However, a number of data‐related issues complicate the use of invertebrate traits for ecological studies. It is uncertain how harmonising varying trait definitions among databases might influence subsequent identification of trait–environment relationships. Furthermore, there have been few comparisons of trait aggregation approaches with expert‐assigned trait affinities. We describe inconsistencies in the definitions of traits used to create freshwater invertebrate trait databases in Europe, North America, New Zealand, and Australia. Based on our comparisons of these databases, we established four novel trait datasets by harmonising definitions of commonly used traits. Next, we used two of these datasets to compare aggregated traits obtained by different aggregation methods with traits assigned by experts, both at the family level. The trait aggregation methods that we compared used either the mean or the median and different weightings. We further explored the effects of harmonisation and trait aggregation by re‐analysing data from a case study. We found that among databases, trait definitions often differed because varying numbers of traits were used to describe particular functions (e.g., respiration traits) and the way those functions were described also varied (e.g., for feeding mode some databases focused on the food source, whereas others focused on mouthpart morphology). The coding to describe traits (binary, fuzzy) also varied among databases. Our comparison of different aggregation methods showed that family‐level aggregated and expert‐assigned traits were similar, especially when traits were aggregated based on the median of trait values of taxa within a family. The case study showed that harmonised and aggregated data identified similar trait–environment relationships to non‐aggregated data. However, harmonised and aggregated data yielded only partially similar values for functional diversity metrics when compared to the case study results. By identifying inconsistencies in trait definitions we hope to motivate the development of standardised definitions for invertebrate traits. Our results also illustrate the usefulness of harmonised datasets for ecological study and provide guidance for the circumstances under which the choice of trait aggregation method is important.

Community Detection in Large-Scale Bipartite Biological Networks.

Networks are useful tools to represent and analyze interactions on a large, or genome-wide scale and have therefore been widely used in biology. Many biological networks—such as those that represent regulatory interactions, drug-gene, or gene-disease associations—are of a bipartite nature, meaning they consist of two different types of nodes, with connections only forming between the different node sets. Analysis of such networks requires methodologies that are specifically designed to handle their bipartite nature. Community structure detection is a method used to identify clusters of nodes in a network. This approach is especially helpful in large-scale biological network analysis, as it can find structure in networks that often resemble a “hairball” of interactions in visualizations. Often, the communities identified in biological networks are enriched for specific biological processes and thus allow one to assign drugs, regulatory molecules, or diseases to such processes. In addition, comparison of community structures between different biological conditions can help to identify how network rewiring may lead to tissue development or disease, for example. In this mini review, we give a theoretical basis of different methods that can be applied to detect communities in bipartite biological networks. We introduce and discuss different scores that can be used to assess the quality of these community structures. We then apply a wide range of methods to a drug-gene interaction network to highlight the strengths and weaknesses of these methods in their application to large-scale, bipartite biological networks.

Diluted Luria-Bertani medium vs. sewage sludge as growth media: comparison of community structure and diversity in the culturable bacteria.

Because colony formation is essential to seek bacterial functions by the direct observation of phenotype, the diversification of colony formation for culturable bacteria is a big challenge in the research field of Environmental Biotechnology. In this study, the biodiversity of cultivable bacteria (colony or liquid culture) was compared by using Luria-Bertani (LB) medium and waste sewage sludge (WSS) under different dilutions and temperatures. When WSS was used as a bacterial source, whereas the highest number of colonies was found at the concentration of WSS (5%), a particular concentration of LB (10%) or WSS (1%) as a growth medium showed the best number of the operational taxonomic units (OTUs) of colonies. The results of bacterial community structure indicated that there are 1, 8, and 12 bacterial genera found uniquely in the agar plates of LB, 10% LB, and 5% WSS. By contrast, when palm oil mill effluent sludge was used as a bacterial source, the effect of dilution was different with WSS. When comparing the biodiversity between colonies and liquid culture, a high OTU value was observed in the colonies on the plate. In addition, 30°C showed the highest number of colonies in LB, 10% LB, and 5% WSS whereas the best OTUs were observed at 37°C for LB and 10% LB, and at 25°C for 5% WSS. This study demonstrates the diversification of cultivable bacteria through the number of OTUs in diluted LB medium and WSS, which is beneficial to isolate a unique bacterial strain.Key points• Impacts of diluted LB medium and WSS for colony formation were determined.• Difference of concentration of LB and WSS made different effects on colony formation.• Temperature change affected on diluted LB and WSS as media.

Comparative fish community structure among different types of enclosures of estuarine environments

This study explores the differences of fish assemblages in three macrotidal estuaries of Man-gyeong River Estuary (MRE), Geum River Estuary (GRE), and Han River Esturay (HRE) with similar ranges of seasonal water temperature that are diked with different levels of disconnection from freshwater discharge. The distribution of major species in the three estuaries could generally be grouped into three distinctive patterns based on their cumulative distribution with respect to the salinity gradient. The MRE was geographically closer to the GRE than to the HRE, but the fish community of the MRE more closely resembled that of the HRE. Increased freshness of the water inside the dike and the limit of coastal fish to the river may have led to this result. The results provide clues to how enclosure patterns of estuarine waters could affect fish communities over a long-term period. In addition, the information may provide guidance for how a fish community may return once environmental conditions are restored.

Cormorants have negligible seascape-scale impacts on benthic vegetation communities

Great cormorant Phalacrocorax carbo sinensis populations in the Baltic Sea have rapidly expanded since the 1990s, raising concerns about their ecosystem impacts. Nutrient runoff from colonies, as well as cormorant predation on fish, can affect surrounding producer communities. Past studies have found cormorant impacts on producers in the immediate vicinity of colonies, but the importance of cormorants over a larger spatial scale is unknown, especially compared to other environmental variables. We used an extensive underwater vegetation inventory dataset (~18000 data points along the Finnish coast) to determine the effects of cormorant colonies on macroalgae and plants. We compared community structure and species abundance/occurrence in near-colony (<5 km from a colony) and control (>10 km from a colony) points, and determined the importance of cormorant influence (using an index incorporating colony size and distance from the colony) in near-colony sites. We found no significant differences in community structure between near-colony and control points in most habitats, and adding the cormorant index only infinitesimally improved statistical models after incorporating other environmental factors. However, the abundance of several species did differ; in particular, the foundation species bladderwrack Fucus vesiculosus and eelgrass Zostera marina were either less likely to occur in near-colony points or were negatively correlated with cormorant index, possibly due to the effects of nutrient enrichment from colonies. Our findings confirm that cormorants can have effects on some producer species, but highlight that these effects are negligible when taking into account the scale and magnitude of other bottom-up and top-down processes occurring in the Baltic Sea.

16S rRNA Gene and Transcript Profiling: an Application on Full-scale Anaerobic Reactors of Wastewater Sludges

Sludge anaerobic digestion is a wastewater treatment plant crucial point for the impact mitigation on environment. Such process reduces the disposable sludge volume and pollution potential, generating biogas. Despite its crucial role, sludge digestion microbiology is not clearly understood. In this work, the characterization of the microbiota into digesters fed by primary and secondary sludges was performed. Two sampling sessions were conducted and more than 120 samples were extracted and analyzed by PCR-DGGE. Cluster analysis on DGGE profiles suggested the presence of diverse communities associated with different sludge characteristics (ANOVA, p < 0.01) and Shannon’s diversity index showed higher evenness into the secondary one. Moreover, the comparison of community structure based on DNA and bacterial rRNA genes highlighted the presence of unexpressed bacterial genome, leading to a potential functionality overestimation using a DNA-based approach (Shannon index mean − 16%, t test, p < 0.05). This approach has proven to be suitable for a first useful assessment of microbial community dynamics during the anaerobic digestion process.

Communities and Attachment Networks Associated with Primary, Secondary and Alternative Foundation Species; A Case Study of Stressed and Disturbed Stands of Southern Bull Kelp

Southern bull kelps (Durvillaea spp., Fucales) are ‘primary’ foundation species that control community structures and ecosystem functions on temperate wave-exposed rocky reefs. However, these large foundation species are threatened by disturbances and stressors, including invasive species, sedimentation and heatwaves. It is unknown whether ‘alternative’ foundation species can replace lost southern bull kelps and its associated communities and networks. We compared community structure (by quantifying abundances of different species) and attachment-interaction networks (by quantifying which species were attached to other species) among plots dominated by Durvillaea spp. and plots where Durvillaea spp. were lost either through long-term repeated experimental removals or by recent stress from a marine heatwave. Long-term experimental removal plots were dominated by ‘alternative’ foundation species, the canopy-forming Cystophora spp. (Fucales), whereas the recent heatwave stressed plots were dominated by the invasive kelp Undaria pinnatifida (Laminariales). A network analysis of attachment interactions showed that communities differed among plots dominated by either Durvillaea spp., Cystophora spp. or U. pinnatifida, with different relationships between the primary, or alternative, foundation species and attached epiphytic ‘secondary’ foundation species. For example, native Cystophora spp. were more important as hosts for secondary foundation species compared to Durvillaea spp. and U. pinnatifida. Instead, Durvillaea spp. facilitated encrusting algae, which in turn provided habitat for gastropods. We conclude that (a) repeated disturbances and strong stressors can reveal ecological differences between primary and alternative foundation species, (b) analyses of abundances and attachment-networks are supplementary methods to identify linkages between primary, alternative and secondary foundation species, and (c) interspersed habitats dominated by different types of foundation species increase system-level biodiversity by supporting different species-abundance patterns and species-attachment networks.

Farmland bird responses to land abandonment in Western Siberia

Land abandonment is an important driver of biodiversity changes. Nearly 60 million ha of cropland and huge areas of managed grassland were abandoned after the collapse of the Soviet Union in 1991. We compared community structure and abundances of farmland birds on used and abandoned cropland, pastures and hay meadows in a study area situated in the Western Siberian crop belt. Abandoned land hosted distinct communities of farmland birds that were similar to those of abandoned farmland elsewhere in the former Soviet Union. More species profited from abandonment than suffered, but the densities of a distinct group of ‘meadow birds’, a group of high conservation concern in Eurasia, were lower on abandoned land compared to managed pastures and hay meadows.Abandoned land had taller, but not denser vegetation and higher plant litter cover than used pastures and hay meadows. The vegetation structure of abandoned land explained differences in bird abundance well, and responses to vegetation parameters were non-linear and species-specific. Future land-use trends are difficult to predict, but cropland recultivation and intensification seem likely. Conservation strategies should entail minimized reclamation of abandoned cropland (perhaps coupled with sustainable intensification on existing farmland), and low-input management of pastures and hay meadows. As a large proportion of the grassland is managed for subsistence farming, measures to slow down further rural human outmigration would also benefit bird biodiversity.

Zooplankton in the Huangyan Atoll, South China Sea: A comparison of community structure between the lagoon and seaward reef slope

Relatively few studies have investigated the community structure of zooplankton in the atolls of the central South China Sea. Zooplankton were sampled at nine stations within the lagoon and four facing the seaward reef-slope in the Huangyan Atoll during May 2015. Lagoonal samples contained 48 zooplankton taxa ( H' =2.25±0.95; J =0.70±0.23) with planktonic larvae, copepods, and euphausids contributing 95.63% of total abundance. Seaward oceanic samples contained 114 zooplankton ( H' =5.27±0.27; J =0.90±0.03) with copepods, siphonophores, chaetognaths, appendicularians, and planktonic larvae accounting for 93.66% of abundance. Lagoonal zooplankton abundance was lower than that on the seaward reef-slope. Zooplankton community differed significantly between the lagoon and reef-slope groups ( R =0.708, P =0.001). The former was dominated by Macruran larvae, Brachyuran larvae, Stylocheiron carinatum, and Acartia spp., while the latter was predominately represented by Oikopleura longicauda, Chelophyes contorta and Copilia mirabilis. Chlorophyll a concentration was significantly higher in the lagoon than the reef slope regions ( P <0.01), which may be due to the nutrient input from fishing vessels near the lagoon mouth. Zooplankton abundance was negatively correlated with chlorophyll a concentration ( P <0.01). A clear difference was observed statistically in the species composition and abundance of zooplankton between the lagoon and the seaward slope at Huangyan Atoll, which suggests that it may be resulted from the influence by natural and anthropogenic interactions.

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium.

Our knowledge of the rhizosphere bacterial communities in deep soils and the role of Eucalyptus and Acacia on the structure of these communities remains very limited. In this study, we targeted the bacterial community along a depth profile (0 to 800 cm) and compared community structure in monospecific or mixed plantations of Acacia mangium and Eucalyptus grandis. We applied quantitative PCR (qPCR) and sequence the V6 region of the 16S rRNA gene to characterize composition of bacterial communities. We identified a decrease in bacterial abundance with soil depth, and differences in community patterns between monospecific and mixed cultivations. Sequence analysis indicated a prevalent effect of soil depth on bacterial communities in the mixed plant cultivation system, and a remarkable differentiation of bacterial communities in areas solely cultivated with Eucalyptus. The groups most influenced by soil depth were Proteobacteria and Acidobacteria (more frequent in samples between 0 and 300 cm). The predominant bacterial groups differentially displayed in the monospecific stands of Eucalyptus were Firmicutes and Proteobacteria. Our results suggest that the addition of an N2-fixing tree in a monospecific cultivation system modulates bacterial community composition even at a great depth. We conclude that co-cultivation systems may represent a key strategy to improve soil resources and to establish more sustainable cultivation of Eucalyptus in Brazil.

Allelopathic effects on the sun-coral invasion: facilitation, inhibition and patterns of local biodiversity

In spite of growing concerns about the invasion of the sun-coral Tubastraea coccinea along the tropical Southwestern Atlantic, the biological interactions mediating this species’ establishment and spread are largely unknown. Here, we identified species associations with T. coccinea by comparing community structure between invaded and non-invaded areas at Buzios Island, SP, Brazil. We also investigated effects of chemical cues from representative benthic species on sun-coral larval performance in the laboratory and quantified the density of sun-coral recruits across different microhabitats in the field. Field surveys showed that the invasion of the sun-coral is more intense at reef areas of higher species richness and diversity, putting at risk a higher number of native species than anticipated and suggesting that local richness offers little resistance to invasion. Highest density of T. coccinea recruits observed on the least bioactive encrusting corallines suggests this taxonomic group may constitute doorways to the establishment of this coral. In contrast, field patterns of sun-coral colonies and recruits, as well as laboratory trials, suggest that cnidarian-dominated habitats represent obstacles to the sun-coral invasion. Thus, while areas dominated by the snowflake coral Carijoa riisei—which showed the greatest negative allelopathic effect on T. coccinea—likely provide resistance to the invader spreading, areas covered by encrusting coralline algae and ‘barren substrates’ probably facilitate its establishment. Because these latter, less-structured microhabitats often prevail after disturbance, damage assessment following human-mediated impacts should include detection and control of sun-coral populations.

Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors.

We sought to investigate the effects of HIV infection on the vaginal microbiota and associations with treatment and demographic factors. We thus compared vaginal microbiome samples from HIV-infected (HIV+) and HIV-uninfected (HIV-) women collected at two Chicago area hospitals. We studied vaginal microbiome samples from 178 women analyzed longitudinally (n = 324 samples) and collected extensive data on clinical status and demographic factors. We used 16S rRNA gene sequencing to characterize the bacterial lineages present, then UniFrac, Shannon diversity, and other measures to compare community structure with sample metadata. Differences in microbiota measures were modest in the comparison of HIV+ and HIV- samples, in contrast to several previous studies, consistent with effective antiretroviral therapy. Proportions of healthy Lactobacillus species were not higher in HIV- patients overall, but were significantly higher when analyzed within each hospital in isolation. Rates of bacterial vaginosis were higher among African-American women and HIV+ women. Bacterial vaginosis was associated with higher frequency of HIV+. Unexpectedly, African-American women were more likely to switch bacterial vaginosis status between sampling times; switching was not associated with HIV+ status. The influence of HIV infection on the vaginal microbiome was modest for this cohort of well suppressed urban American women, consistent with effective antiretroviral therapy. HIV+ was found to be associated with bacterial vaginosis. Although bacterial vaginosis has previously been associated with HIV transmission, most of the women studied here became HIV+ many years before our test for bacterial vaginosis, thus implicating additional mechanisms linking HIV infection and bacterial vaginosis.

Comparison of community structure and growth between the alpine dwarf shrubs Rhododendron aureum and R. brachycarpum on the Yatsugatake range, central Japan

Comparison of community structure and growth between the alpine dwarf shrubs Rhododendron aureum and R. brachycarpum on the Yatsugatake range, central Japan

Comparison of community structures between particle-associated and free-living prokaryotes in tropical and subtropical Pacific Ocean surface waters

The subtropical and tropical regions of the Pacific Ocean are less productive than other oceanic regions. Although particle association should be an important strategy for heterotrophic prokaryotes to survive in such environments, we have little information on particle-associated (PA) prokaryotes in these regions. The specific aim of this study was to determine bacterial and archaeal community structures in the PA assemblage in comparison to the free-living (FL) assemblage in the North Pacific Subtropical Gyre, the South Pacific Subtropical Gyre, and an eastern equatorial region of the Pacific Ocean. Community profiles and phylogenetic identities were obtained by denaturing gradient gel electrophoresis, 454-pyrosequencing, and cloning followed by Sanger sequencing of 16Sr RNA gene amplicons. The distribution patterns of some abundant groups in three regions and two lifestyles (PA and FL) are shown in this study. Also, the PA community structures of bacteria differed from the FL ones and exhibited higher diversity than the FL ones, while the archaeal community structures did not show significant differences between PA and FL assemblages. We found that specific phylotypes of Gammaproteobacteria and Flavobacteria were abundant in PA bacterial assemblages, suggesting that they prefer to attach and consume particulate organic matter. In summary, the surface seawater PA assemblages represent very different bacterial and archaeal community structures between three different oceanic regions, each of which had distinct PA and FL community structures. These results imply that environmental factors determine microbial community structures.

Microbial Diversity in Continuous Flow Constructed a Wetland for the Treatment of Swine Waste

Contaminant removal may largely be a function of many microbial processes in constructed wetlands. However, the role of microbial diversity for the removal of swine waste in constructed wetlands is limited. Here, we used 454/ GS-FLX pyrosequencing to assess archaeal, bacterial, and fungal composition within a surface flow constructed wetland to determine their spatial dynamics and contaminant removal within the wetland. We analyzed our data using UniFrac and principal coordinate analysis (PCoA) to compare community structure and specific functional groups of bacteria, archaea, and fungi in different sections of the wetland. PCoA analysis showed that, bacterial, archaeal, and fungal composition were significantly different (p=0.001) for the influent compared to the final effluent. Our results showed that, the wetland system contained relatively higher proportions of bacteria and fungi than archaea. Most of the bacteria and archaea that were associated with nitrogen removal were affiliated with Nitrosomonas which are ammonia oxidizing bacteria (AOB), Candidatus Solibacter, an anaerobic ammonia oxidizing bacteria (Anammox), as well as Nitrosopumilus, ammonia oxidizing archaea (AOA). The detection of AOB, Anammox, and AOA in this wetland shows abundance and diversity of these microorganisms that are responsible for nitrification processes in constructed wetlands.

Influence of inorganic fertilizer and organic manure application on fungal communities in a long-term field experiment of Chinese Mollisols

The effects of 35 years of manure amendment on fungal communities were evaluated in Mollisols of northeast China. Soil samples from different fertilization regimes were collected, and quantitative PCR analysis of fungal community size and Illumina platform based analysis of the ITS gene were performed to characterize soil fungal abundance and compare community structure and diversity. The treatments were no fertilizer (CK); manure (M); nitrogen, phosphorus and potassium inorganic fertilizer (NPK); and inorganic fertilizer plus manure (MNPK) regimes. Soil fungal diversity was decreased by inorganic fertilizer. Inorganic fertilizer plus manure induced a weak increase in fungal diversity and a slight decrease in size. The predominant phyla were Ascomycota (63.77–78.70%), Zygomycota (8.33–14.80%) and Basidiomycota (4.03–13.47%). At each taxonomic level, the percentages dramatically differed, especially between MNPK and NPK. For example, the numbers of Fusarium and Gibberella with potential pathogenicity were all higher in NPK than in MNPK; the beneficial genus Podospora was the highest in MNPK and the least in NPK. Principal coordinates analysis showed that CK and M were clustered together; the incorporation of NPK with manure improved the fungal structure near to that of CK and separate from that of NPK. Redundancy analysis indicated that fungal community structure was most affected by soil available phosphorus (AP) and organic matter contents, followed by soil pH. Simpson and Shannon indices were closely correlated with soil pH, AP, total phosphorus and total nitrogen. The results indicated that manure application altered soil properties and soil fungal community structure, and manure with inorganic fertilizer counteracted some of the adverse effects of the inorganic fertilizer.