Benthic community resilience in two differently impacted tropical estuaries: Taxonomic vs functional approaches.

Estuaries experience incessant modifications due to various stressors causing shifts in the benthic species community structure and ecosystem functioning. Two tropical estuaries along Northwest India, exposed to varied intensities of anthropogenic perturbations, were sampled seasonally for two consecutive years. Specific aims were to assess, compare and link the macroinvertebrate taxonomic and functional structures, to evaluate the resilience of estuarine benthic ecosystems by employing the multiple-trait approach and to identify major influencing environmental drivers for patterns discerned. Taxonomic and functional compositions in both the estuaries produced varied segregations along the estuarine zones, driven primarily by natural estuarine gradients like salinity and sediment grain size, despite extant anthropogenic stressors. Multiple traits contributed to the variance in benthic functioning. The Biological Trait Analysis (BTA) revealed that both the estuaries had similar trait compositions in the lower zones, while the middle and upper zones of each estuary presented different permutations of traits. The functional complexity at different estuarine sections was influenced by the variability in taxonomic composition and species dominance. However, relationships between Functional Diversity (FD) and species diversity were equivocal, signifying that taxonomic diversity may not be an efficient proxy for benthic functioning. As the zones had differential stressors and disturbance acts as a filter, discrete functional trait profiles of opportunistic traits were visualized along the potentially impacted zones. Thus, the less impacted lower zones had multiple traits, while the mid-upper zones that were subject to both anthropogenic and natural stressors had fewer traits. A more consistent functional structure, higher functional redundancy and substantial proportion of recolonisation traits (small-sized, short-lived, motile forms) suggested better resilience in one study estuary than the other one. Our study advocates that the inclusion of both taxonomical and functional metrics can provide in-depth inferences related to the macrobenthic community resilience and this coupled approach is imperative for effective future management programs.

Candidemia in cancer patients: features of the taxonomic structure.

The aim of the study was to determine the main Candida species isolated from blood of cancer patients, to compare the taxonomic structure of strains obtained from children and adults with candidemia. In total, during the study period, candidemia was microbiologically proven by blood culture in 81 patients (duplicates were excluded). Patients in the intensive care unit (ICU) accounted for 35,8%. The total number of isolates elaborated was 82 strains of 10 Candida species. In general, in the taxonomic structure of candidemias, C. parapsilosis (61.0%) predominates, C. albicans (20.7%) is in the second place, followed by C. glabrata and C. lusitaniae (3.7% each); C. krusei, C. guilliermondii and C. tropicalis (2.4% each). C. parapsilosis was statistically significantly often isolated from blood compared to C. albicans (61.0% versus 20.7%, respectively, p<0.0001). Candidemia was statistically significantly more often detected in adults than in children (63.0% versus 37.0%, respectively, p<0.002). Moreover, in adults, C. parapsilosis was statistically significantly more often isolated from blood than C. albicans (70.6% versus 15.7%, respectively, p<0.0001). In children, there were no significant differences in the frequency of isolation of C. parapsilosis and C. albicans: the proportion of C. parapsilosis was 45.2%, C. albicans - 29.0%. Rare species were identified in 7.8% of cases in adults, and in 12.9% of cases in children without statistical difference (p>0.05). The proportion of Candida non-albicans during the study period was 79.3%, and C. parapsilosis is the main species in this group (76.9%).

Do river basins influence the composition of functional traits of fish assemblages in Neotropical reservoirs? / As bacias hidrográficas influenciam a composição funcional da assembleia de peixes em reservatórios da região Neotropical?

Abstract In aquatic environments, dams are considered one of the main threats to fish species, acting as an environmental filter for certain functional traits. Although there is some predictability in the composition of the functional traits in reservoirs, it is hypothesized that the environmental filters imposed by evolutionary processes, linked to the characteristics of the basins, are determinant for the functional composition of the traits in reservoirs. For this we performed a PCoA using the functional traits composition matrix of the reservoirs. We used PERMANOVA to test the difference in functional composition between basins. We performed the same process for the species composition matrix to compare the patterns. In this study, there were taxonomic and functional differences among reservoirs inserted in different basins. It was observed that the basin is a determining factor for the functional structure of fish assemblage in reservoirs. When compared, functional and taxonomic structures follow the same pattern, although functionally the reservoir tends to be more similar. These results reinforce the idea that reservoirs act as filters for functional traits (e.g., related with reproduction, feeding and habitat use), although there is a great influence of evolutionary processes related to the basin's characteristics and origin of the ichthyofaunistic province.

Resumo Em ambientes aquáticos, a construção de barragens é considerada uma das principais ameaças para as espécies de peixes, atuando como filtro ambiental para determinados traços funcionais. Assim, embora exista certa previsibilidade na composição dos traços funcionais em reservatórios, é hipotetizado que os filtros ambientais impostos pelos processos evolutivos, ligados as características das bacias, são determinantes para a composição funcional dos traços nos reservatórios. Para isso realizamos uma PCoA utilizando a matriz de composição de traços funcionais dos reservatórios. Utilizamos a PERMANOVA para testar a diferença da composição funcional entre as bacias. Realizamos o mesmo processo para a matriz de composição de espécies para comparar os padrões. Foi possível observar que a bacia hidrográfica é um fator determinante para a estruturação funcional da assembleia de peixe em reservatórios. Quando comparadas, a estrutura funcional e taxonômica, ambas seguem o mesmo padrão, embora funcionalmente os ambientes tendem a ser mais semelhantes. Esses resultados reforçam a ideia de que reservatórios atuam como filtros para determinados traços funcionais (e.g., relacionados à reprodução, alimentação e uso de habitat), embora exista uma grande influência dos processos evolutivos ligados a característica da bacia e da origem da província ictiofaunística.

Integrated metagenomic and metatranscriptomic analyses of ultraviolet disinfection effects on antibiotic resistance genes and bacterial communities during wastewater treatment.

Ultraviolet (UV) disinfection is now widely implemented in wastewater treatment plants (WWTPs) worldwide, but its effect on antibiotic resistome of the surviving bacteria remains unclear. In this study, we employed high-throughput sequencing-based metagenomic and metatranscriptomic approaches to comprehensively elucidate the effects of UV disinfection on the shifts of bacterial community and antibiotic resistance genes (ARGs) on both DNA and mRNA levels in one WWTP. Metagenomic analyses revealed an insignificant change in the bacterial community after UV disinfection, while metatranscriptomic analyses showed that UV disinfection significantly changed the abundance of 13.79% of phyla and 10.32% of genera. In total, 38 ARG-like open reading frames (ORFs) and 327 ARG-like transcripts were identified in the DNA and RNA samples, respectively. The relative abundances of the total ARGs, each ARG type, and each ARG subtype also varied after UV disinfection. Additionally, UV disinfection significantly reduced the expression of total ARGs from 49.40 transcripts per kilobase of exon model per million mapped reads (TPM) to 47.62 TPM, and significantly changed the expression of 10.75% of ARG subtypes in wastewater (p < 0.05). Notably, the significant increase in the expression and obvious increase in the relative abundance of macrolide-lincosamide-streptogramin B (MLSB) resistance genes revealed that UV disinfection increases the potential health risk of MLSB resistance genes in wastewater. Moreover, potential host analyses of ARGs revealed the different preferences of antibiotic resistant bacteria (ARB) to ARGs. This study may shed new light on the underlying mechanism of the UV disinfection effect on antibiotic resistance.

Degraded functional structure of macroinvertebrates caused by commercial sand dredging practices in a flood plain lake.

In parts of developing countries, the over-exploitation of sands from inland waters has led to serious environmental concerns. However, understanding of the impacts of commercial sand dredging on inland water ecosystem functions remains limited. Herein, we assess the effects of this activity on the functional structure of the macroinvertebrate community and its recovery processes based on a 4-year survey, in the South Dongting Lake in China. Our result showed a simplified macroinvertebrate functional structures within the dredged area, as evidenced by a loss of certain trait categories (e.g., oval and conical body form) and a significant reduction in trait values due to the direct removal of macroinvertebrates and indirect alternations to physical environmental conditions (e.g., water depth and %Medium sand). Moreover, clear increases were observed in certain trait categories (e.g., small body size and swimmer) resulting from the dredging-related disturbance (e.g., increased turbidity) within the adjacent area. Furthermore, one year after the cessation of dredging, a marked recovery in the taxonomic and functional structure of macroinvertebrate assemblages was observed with most lost trait categories returning and an increase in the trait values of eight categories (e.g., body size 1.00-3.00 cm and oval body form) within the dredged and adjacent area. In addition, dispersal processes and sediment composition were the main driver for the structuring of the macroinvertebrate taxonomic and functional assemblages during the dredging stages, whilst water environmental conditions dominated the taxonomic structure and dispersal processes determined the functional structure during the recovery stage. Implications of our results for monitoring and management of this activity in inland waters are discussed.

Metataxonomic and metagenomic analysis of mangrove microbiomes reveals community patterns driven by salinity and pH gradients in Paranaguá Bay, Brazil.

While environmental drivers regulate the structure of mangrove microbial communities, their exact nature and the extent of their influence require further elucidation. By means of 16S rRNA gene-based sequencing, we determined the microbial taxonomic profiles of mangroves in the subtropical Paranaguá Bay, Brazil, considering as potential drivers: salinity, as represented by two sectors in the extremes of a salinity gradient (<5 PSU and >30 PSU); proximity to/absence of the prevailing plants, Avicennia schaueriana, Laguncularia racemosa, Rhizophora mangle, and Spartina alterniflora; and the chemical composition of the sediments. Salinity levels within the estuary had the strongest influence on microbial structure, and pH was important to separate two communities within the high salinity environment. About one fourth of the total variation in community structure resulted from covariation of salinity and the overall chemical composition, which might indicate that the chemical profile was also related to salinity. The most prevalent bacterial phyla associated with the mangrove soils analyzed included Proteobacteria, Actinobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Cyanobacteria. Taxonomic and functional comparisons of our results for whole-genome sequencing with available data from other biomes showed that the studied microbiomes cluster first according to biome type, then to matrix type and salinity status. Metabolic functions were more conserved than organisms within mangroves and across all biomes, indicating that core functions are preserved in any of the given conditions regardless of the specific organisms harboring them.

Analysing taxonomic structures and local ecological processes in temperate forests in North Eastern China.

BACKGROUND: One of the core issues of forest community ecology is the exploration of how ecological processes affect community structure. The relative importance of different processes is still under debate. This study addresses four questions: (1) how is the taxonomic structure of a forest community affected by spatial scale? (2) does the taxonomic structure reveal effects of local processes such as environmental filtering, dispersal limitation or interspecific competition at a local scale? (3) does the effect of local processes on the taxonomic structure vary with the spatial scale? (4) does the analysis based on taxonomic structures provide similar insights when compared with the use of phylogenetic information? Based on the data collected in two large forest observational field studies, the taxonomic structures of the plant communities were analyzed at different sampling scales using taxonomic ratios (number of genera/number of species, number of families/number of species), and the relationship between the number of higher taxa and the number of species. Two random null models were used and the "standardized effect size" (SES) of taxonomic ratios was calculated, to assess possible differences between the observed and simulated taxonomic structures, which may be caused by specific ecological processes. We further applied a phylogeny-based method to compare results with those of the taxonomic approach. RESULTS: As expected, the taxonomic ratios decline with increasing grain size. The quantitative relationship between genera/families and species, described by a linearized power function, showed a good fit. With the exception of the family-species relationship in the Jiaohe study area, the exponents of the genus/family-species relationships did not show any scale dependent effects. The taxonomic ratios of the observed communities had significantly lower values than those of the simulated random community under the test of two null models at almost all scales. Null Model 2 which considered the spatial dispersion of species generated a taxonomic structure which proved to be more consistent with that in the observed community. As sampling sizes increased from 20 m × 20 m to 50 m × 50 m, the magnitudes of SESs of taxonomic ratios increased. Based on the phylogenetic analysis, we found that the Jiaohe plot was phylogenetically clustered at almost all scales. We detected significant phylogenetically overdispersion at the 20 m × 20 m and 30 m × 30 m scales in the Liangshui plot. CONCLUSIONS: The results suggest that the effect of abiotic filtering is greater than the effects of interspecific competition in shaping the local community at almost all scales. Local processes influence the taxonomic structures, but their combined effects vary with the spatial scale. The taxonomic approach provides similar insights as the phylogenetic approach, especially when we applied a more conservative null model. Analysing taxonomic structure may be a useful tool for communities where well-resolved phylogenetic data are not available.

Soil DNA Extraction Procedure Influences Protist 18S rRNA Gene Community Profiling Outcome.

Advances in sequencing technologies allow deeper studies of the soil protist diversity and function. However, little attention has been given to the impact of the chosen soil DNA extraction procedure to the overall results. We examined the effect of three acknowledged DNA recovery methods, two manual methods (ISOm-11063, GnS-GII) and one commercial kit (MoBio), on soil protist community structures obtained from different sites with different land uses. Results from 18S rRNA gene amplicon sequencing suggest that DNA extraction method significantly affect the replicate homogeneity, the total number of operational taxonomic units (OTUs) recovered and the overall taxonomic structure and diversity of soil protist communities. However, DNA extraction effects did not overwhelm the natural variation among samples, as the community data still strongly grouped by geographical location. The commercial DNA extraction kit was associated with the highest diversity estimates and with a corresponding higher retrieval of Excavata, Cercozoa and Amoebozoa-related taxa. Overall, our findings indicate that this extraction offers a compromise between rare and dominant taxa representation, while providing high replication reproducibility. A comprehensive understanding of the DNA extraction techniques impact on soil protist diversity can enable more accurate diversity assays.

A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping.

BACKGROUND: The role of the microbiota in human health and disease has been increasingly studied, gathering momentum through the use of high-throughput technologies. Further identification of the roles of specific microbes is necessary to better understand the mechanisms involved in diseases related to microbiome perturbations. METHODS: Here, we introduce a new microbiome-based group association testing method, optimal microbiome-based association test (OMiAT). OMiAT is a data-driven testing method which takes an optimal test throughout different tests from the sum of powered score tests (SPU) and microbiome regression-based kernel association test (MiRKAT). We illustrate that OMiAT efficiently discovers significant association signals arising from varying microbial abundances and different relative contributions from microbial abundance and phylogenetic information. We also propose a way to apply it to fine-mapping of diverse upper-level taxa at different taxonomic ranks (e.g., phylum, class, order, family, and genus), as well as the entire microbial community, within a newly introduced microbial taxa discovery framework, microbiome comprehensive association mapping (MiCAM). RESULTS: Our extensive simulations demonstrate that OMiAT is highly robust and powerful compared with other existing methods, while correctly controlling type I error rates. Our real data analyses also confirm that MiCAM is especially efficient for the assessment of upper-level taxa by integrating OMiAT as a group analytic method. CONCLUSIONS: OMiAT is attractive in practice due to the high complexity of microbiome data and the unknown true nature of the state. MiCAM also provides a hierarchical association map for numerous microbial taxa and can also be used as a guideline for further investigation on the roles of discovered taxa in human health and disease.

Do river basins influence the composition of functional traits of fish assemblages in Neotropical reservoirs?

Abstract In aquatic environments, dams are considered one of the main threats to fish species, acting as an environmental filter for certain functional traits. Although there is some predictability in the composition of the functional traits in reservoirs, it is hypothesized that the environmental filters imposed by evolutionary processes, linked to the characteristics of the basins, are determinant for the functional composition of the traits in reservoirs. For this we performed a PCoA using the functional traits composition matrix of the reservoirs. We used PERMANOVA to test the difference in functional composition between basins. We performed the same process for the species composition matrix to compare the patterns. In this study, there were taxonomic and functional differences among reservoirs inserted in different basins. It was observed that the basin is a determining factor for the functional structure of fish assemblage in reservoirs. When compared, functional and taxonomic structures follow the same pattern, although functionally the reservoir tends to be more similar. These results reinforce the idea that reservoirs act as filters for functional traits (e.g., related with reproduction, feeding and habitat use), although there is a great influence of evolutionary processes related to the basins characteristics and origin of the ichthyofaunistic province.

Resumo Em ambientes aquáticos, a construção de barragens é considerada uma das principais ameaças para as espécies de peixes, atuando como filtro ambiental para determinados traços funcionais. Assim, embora exista certa previsibilidade na composição dos traços funcionais em reservatórios, é hipotetizado que os filtros ambientais impostos pelos processos evolutivos, ligados as características das bacias, são determinantes para a composição funcional dos traços nos reservatórios. Para isso realizamos uma PCoA utilizando a matriz de composição de traços funcionais dos reservatórios. Utilizamos a PERMANOVA para testar a diferença da composição funcional entre as bacias. Realizamos o mesmo processo para a matriz de composição de espécies para comparar os padrões. Foi possível observar que a bacia hidrográfica é um fator determinante para a estruturação funcional da assembleia de peixe em reservatórios. Quando comparadas, a estrutura funcional e taxonômica, ambas seguem o mesmo padrão, embora funcionalmente os ambientes tendem a ser mais semelhantes. Esses resultados reforçam a ideia de que reservatórios atuam como filtros para determinados traços funcionais (e.g., relacionados à reprodução, alimentação e uso de habitat), embora exista uma grande influência dos processos evolutivos ligados a característica da bacia e da origem da província ictiofaunística.

A metagenomic study of the microbial communities in four parallel biogas reactors.

BACKGROUND: Biogas is a renewable energy carrier which is used for heat and power production or, in the form of purified methane, as a vehicle fuel. The formation of methane from organic materials is carried out by a mixed microbial community under anaerobic conditions. However, details about the microbes involved and their function are limited. In this study we compare the metagenomes of four parallel biogas reactors digesting a protein-rich substrate, relate microbiology to biogas performance, and observe differences in these reactors' microbial communities compared to the original inoculum culture. RESULTS: The biogas process performance during the startup phase of four parallel continuous stirred tank reactors (designated R1, R2, R3, and R4) co-digesting fish waste and cow manure was studied. The microbial composition of the inoculum (day 0) and the four reactors at day 59 was studied and compared using 454 FLX Titanium pyrosequencing. In the inoculum and the reactor samples, the Bacteria Clostridium and Syntrophomonas were highly abundant, and the dominating methanogen was the hydrogenotrophic Methanoculleus. Syntrophic prokaryotes frequently found in biogas reactors with high concentrations of ammonium and volatile fatty acids were detected in all samples. The species Candidatus Cloacimonas acidaminovorans of the candidate phylum Cloacimonetes (WWE1) increased in all reactors and was the dominating bacterium at day 59. In particular, this bacterium showed a very high abundance in R1, which distinguished this reactor significantly from the other reactors in terms of microbial composition. Methane production and the reactor slurry characteristics were monitored in the digestion period. Generally all four reactors operated stably and showed rather similar characteristics. The average methane production in the reactors varied between 0.278 and 0.296 L gVS(-1), with the lowest production in R1. CONCLUSIONS: This study showed that four parallel reactors co-digesting manure and fish waste silage operated stably during a startup phase. Several important Archaea and Bacteria degrading the protein-rich substrate were identified. In particular, microorganisms involved in syntrophic methane production seemed to be important. The detailed characterization of the microbial communities presented in this work may be useful for the operation of biogas plants degrading substrates with high concentrations of proteins.

Long-term temporal variation in the organization of an ant-plant network.

BACKGROUND AND AIMS: Functional groups of species interact and coevolve in space and time, forming complex networks of interacting species. A long-term study of temporal variation of an ant-plant network is presented with the aims of: (1) depicting its structural changes over a 20-year period; (2) detailing temporal variation in network topology, as revealed by nestedness and modularity analysis and other parameters (i.e. connectance, niche overlap); and (3) identifying long-term turnover in taxonomic structure (i.e. switches in ant resource use or plant visitor assemblages according to taxa). METHODS: Fieldwork was carried out at La Mancha, Mexico, and ant-plant interactions were observed between 1989 and 1991, between 1998 and 2000, and between May 2010 and 2011. Occurrences of ants on extrafloral nectaries (EFNs) were recorded. The resulting ant-plant networks were constructed from qualitative presence-absence data determined by a species-species matrix defined by the frequency of occurrence of each pairwise ant-plant interaction. KEY RESULTS: Network variation across time was stable and a persistent nested structure may have contributed to the maintenance of resilient and species-rich communities. Modularity was lower than expected, especially in the most recent networks, indicating that the community exhibited high overlap among interacting species (e.g. few species were hubs in the more recent network, being partly responsible for the nested pattern). Structurally, the connections created among modules by super-generalists gave cohesion to subsets of species that otherwise would remain unconnected. This may have allowed an increasing cascade-effect of evolutionary events among modules. Mutualistic ant-plant interactions were structured 20 years ago mainly by the subdominant nectarivorous ant species Camponotus planatus and Crematogaster brevispinosa, which monopolized the best extrafloral nectar resources and out-competed other species with broader feeding habits. Through time, these ants, which are still present, lost their position as network hubs and diminished in their importance in structuring the network; simultaneously, plants gained in importance. CONCLUSIONS: The long-term network analysis reveals a decrease in attended plant species richness, a notable increase in plant species participation from 1990 to 2010 (sustained by less plant taxonomic similarity in the older 1990 network), an increase in the number of ant species and a diminishing dominance of super-generalist ants. The structure of the community has remained highly nested and connected with low modularity, suggesting overall a more participative, homogeneous, cohesive interaction network. Although previous studies have suggested that interactions between ants and EFN-bearing plants are susceptible to seasonality, abiotic factors and perturbation, this cohesive structure appears to be the key for biodiversity and community maintenance.