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Aim Although biodiversity is in sharp decline around the globe, collectiing precise information on changes in overall species richness remains extremely challenging. Efficient and reliable proxy methods are therefore needed, with the diversity of higher taxa representing one such potential proxy for species‐level diversity. Nonetheless, the stability of using this measure across different regions and animal taxa at the global scale has never been investigated thoroughly. Location Global. Time period Up to 2016. Major taxa studied Animalia. Methods We used a large global dataset containing published studies on diversity in the terrestrial Animalia to analyse the relationship between diversity at the family, genus and species level across different orders. Results Family and species diversity were positively correlated, with the strongest correlations in Diptera, Hemiptera and Coleoptera. Correlations were slightly weaker in family–species than in genus–species relationships, whereas differences were stronger in observed richness than in diversity indices. Across all taxa, family–species correlations of Shannon diversity index values were independent of sample size, and they showed limited variation across biomes for the three orders containing sufficient case studies for this analysis. Based on the Shannon diversity index, the species diversity per site increased linearly with the increase in family diversity, with an average species : family diversity index ratio of 2.5, slightly lower than the ratio of 2.7 for observed species and family richness values. Main conclusions Our study confirmed that recording family‐level diversity can be a meaningful proxy for determining species‐level diversity patterns in biodiversity studies, and trade‐offs between identification costs and retained information content need to be considered when using higher taxon surrogacy.

Phytopathogens have developed elaborate mechanisms to attenuate the defense response of their host plants, including convergent evolution of complex pathways for production of the GA phytohormones, which were actually first isolated from the rice fungal pathogen Gibberella fujikuroi. The rice bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) has been demonstrated to contain a biosynthetic operon with cyclases capable of producing the universal GA precursor ent-kaurene. Genetic (knock-out) studies indicate that the derived diterpenoid serves as a virulence factor for this rice leaf streak pathogen, serving to reduce the jasmonic acid-mediated defense response. Here the functions of the remaining genes in the Xoc operon are elucidated and the distribution of the operon in X. oryzae is investigated in over 100 isolates. The Xoc operon leads to production of the bioactive GA4, an additional step beyond production of the penultimate precursor GA9 mediated by the homologous operons recently characterized from rhizobia. Moreover, this GA biosynthetic operon was found to be widespread in Xoc (> 90%), but absent in the other major X. oryzae pathovar. These results indicate selective pressure for production of GA4 in the distinct lifestyle of Xoc, and the importance of GA to both fungal and bacterial pathogens of rice.

AIM: Body size variation in animal assemblages is a widely addressed pattern in biogeographical studies, and is affected by both environmental gradients and phylogenetic constraints. However, no study has yet explored to what extent the association between body size variation and environmental gradients across broad spatial scales is influenced by the biogeographical distribution of different phylogenetic lineages. In this study, we discriminate the influences of environmental variables and phylogenetic community composition on body size variation in South American sigmodontine rodents. LOCATION: South America. METHODS: We computed the mean body mass of sigmodontine species co‐occurring in 1 × 1° cells across South America. For each cell we recorded mean values for three environmental variables. We characterized the phylogenetic composition of sigmodontine assemblages within each cell using phylogenetic fuzzy‐weighting and principal coordinates of phylogenetic structure (PCPS). We then partitioned out the influence of environmental factors and the phylogenetic community composition on mean body size. RESULTS: Mean body size variation was mostly explained by shared influence of phylogenetic community composition (PCPS) and environmental factors (68%), while exclusive influence of PCPS was low (19%), and of environment was even lower (0.47%). Increases in body size were related to increases in annual mean temperature, and the influence of environment on body size was mediated by the distribution of sigmodontine lineages across South America. MAIN CONCLUSIONS: Environment alone was not sufficient to explain body size variation in sigmodontine assemblages. Rather, environmental gradients interacted with historical processes to determine body size variation in the Neotropical assemblages. These results have implications for the way we think of body size gradients across species assemblages, because any gradient in a trait may be a result of differences in the biogeographical distribution of lineages across space, which should be considered in an explicit context.

Purpose To understand which environmental factors influence the distribution and ecological functions of bacteria in agricultural soil. Method A broad range of farmland soils was sampled from 206 locations in Jilin province, China. We used 16S rRNA gene-based Illumina HiSeq sequencing to estimated soil bacterial community structure and functions. Result The dominant taxa in terms of abundance were found to be, Actinobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, and Proteobacteria. Bacterial communities were dominantly affected by soil pH, whereas soil organic carbon did not have a significant influence on bacterial communities. Soil pH was significantly positively correlated with bacterial operational taxonomic unit abundance and soil bacterial α-diversity (P<0.05) spatially rather than with soil nutrients. Bacterial functions were estimated using FAPROTAX, and the relative abundance of anaerobic and aerobic chemoheterotrophs, and nitrifying bacteria was 27.66%, 26.14%, and 6.87%, respectively, of the total bacterial community. Generally, the results indicate that soil pH is more important than nutrients in shaping bacterial communities in agricultural soils, including their ecological functions and biogeographic distribution.

PurposeNitrate (NO3−) is the second preferred terminal electron acceptor after oxygen (O2), as it plays an essential role as the main electron acceptor for respiration under oxygen-depleted conditions. Dissimilatory nitrate reduction to ammonium (DNRA) is an increasingly important process of microbial-driven nitrate reduction in wetland ecosystems, making it necessary to study the biogeographical distribution and structure of the DNRA community, and to identify the factors governing DNRA in global wetlands.Materials and methodsWe collected samples from 15 wetland sites around the world and used qPCR assay analysis to quantify the DNRA functional gene nrfA. High-throughput sequencing was conducted to analyze the microbial diversity and community structure of DNRA bacteria. The most connected genera were derived from molecular ecological network analysis. Principal coordinates analysis (PCoA), redundancy analysis (RDA), and Pearson’s correlation analysis were used to explore the relationship between microbial structure and environmental factors.Results and discussionThe environmental conditions of the wetlands varied largely with the latitude. At the phylum level, Proteobacteria was dominant, and Anaerolinea was the key genus. Pearson’s correlation analysis also illustrated that the annual average temperature, as a factor of latitude, most significantly affected DNRA abundance, followed by total organic matter (TOM) and C/N ratio.ConclusionsFor the first time, we summarized the characteristics of DNRA bacteria at the molecular level, along with the influencing factors, in wetlands with a wide biogeographical distribution. This study provides a scientific foundation for the future study of DNRA bacteria in wetlands around the world.

Marine epizoic diatom, Protoraphis atlantica is reported for the first time in coastal waters off Kasargod and open ocean waters off Kannur along the southeastern Arabian Sea. Diatoms infested exclusively the urosome of calanoid copepods Labidocera sp. and Candacia catula. The taxonomic description, ecological habit, and distribution of Protoraphis are described in the present paper along with microscopical analyses. With the present report from the southeastern Arabian Sea, the geographical distribution of Protoraphis can be extended to Indian waters.

To assess and analyse accurately their geographical distributions, fiddler crabs (Uca) from the Atlantic coast of Brazil were studied using field collections, museum specimens and literature reports. More than 7000 specimens of ten Uca species were collected across five coastal biomes from 63 sites on the Atlantic coast of South America between the Brazilian States of Amapá and Santa Catarina in 2009 and 2010. Based on our analyses of mouthparts and habitat osmolality (=salinity), each species seems to prefer a particular niche defined by a specific array of physical factors. The species' distributions form four geographical patterns along the South Atlantic coast; however, the different species do not occur uniformly within each biome. Most common are U. (M.) rapax, U. (L.) leptodactyla, U. (B.) thayeri and U. (U.) maracoani with the relative abundance of each varying among the biomes according to habitat availability. Owing to their high constituent diversity, two geographical areas are candidates for biological conservation efforts. Considering fossil records, molecular clocks, oceanic hydrology and plate tectonics over the last 65 million years, the biogeographical patterns of the extant species can be used to reconstruct an evolutionary scenario for Uca in the tropical and temperate zones of the western Atlantic Ocean.

Background The broad-leaved Korean pine mixed forest is an important and typical component of a global temperate forest. Soil microbes are the main driver of biogeochemical cycling in this forest ecosystem and have complex interactions with carbon (C) and nitrogen (N) components in the soil. Results We investigated the vertical soil microbial community structure in a primary Korean pine-broadleaved mixed forest in Changbai Mountain (from 699 to 1177 m) and analyzed the relationship between the microbial community and both C and N components in the soil. The results showed that the total phospholipid fatty acid (PLFA) of soil microbes and Gram-negative bacteria (G-), Gram-positive bacteria (G+), fungi (F), arbuscular mycorrhizal fungi (AMF), and Actinomycetes varied significantly ( p  < 0.05) at different sites (elevations). The ratio of fungal PLFAs to bacterial PLFAs (F/B) was higher at site H1, and H2. The relationship between microbial community composition and geographic distance did not show a distance-decay pattern. The coefficients of variation for bacteria were maximum among different sites (elevations). Total soil organic carbon (TOC), total nitrogen (TN), soil water content (W), and the ratio of breast-height basal area of coniferous trees to that of broad-leaved tree species (RBA) were the main contributors to the variation observed in each subgroup of microbial PLFAs. The structure equation model showed that TOC had a significant direct effect on bacterial biomass and an indirect effect upon bacterial and fungal biomass via soil readily oxidized organic carbon (ROC). No significant relationship was observed between soil N fraction and the biomass of fungi and bacteria. Conclusion The total PLFAs (tPLFA) and PLFAs of soil microbes, including G-, G+, F, AMF, and Actinomycetes, were significantly affected by elevation. Bacteria were more sensitive to changes in elevation than other microbes. Environmental heterogeneity was the main factor affecting the geographical distribution pattern of microbial community structure. TOC, TN, W and RBA were the main driving factors for the change in soil microbial biomass. C fraction was the main factor affecting the biomass of fungi and bacteria and ROC was one of the main sources of the microbial-derived C pool.

Aim We analysed the effects of grazing on the diversity and structure of dung beetle communities to see whether the biogeographical and ecological contexts influence dung beetle responses. We hypothesized that the responses of dung beetle communities are modulated by both the ecological conditions resulting from the transformation of native vegetation into grazing areas, and the history of the species inhabiting different biogeographical provinces. Location The state of Hidalgo, in the Mexican Transition Zone, central Mexico. Methods We used a standardized hierarchical sampling procedure in three biogeographical provinces located in Hidalgo. Within each province, we identified the dominant vegetation types, and within these we identified the sites with native vegetation and those modified by grazing. The design included 800 baited pitfall traps, and allowed us to study the response of dung beetle communities with different biogeographical histories to ecological context. Results We captured 8707 beetles belonging to 37 species and 17 genera in the subfamily Scarabaeinae. We found that grazing areas only had a negative effect on dung beetle diversity in tropical forest; conversely, in dry environments (pine–oak forest and xerophilous scrubland) diversity in grazing areas was higher than in the native vegetation sites. We did not detect a clear effect in cloud forest sites. Species turnover between the native vegetation and pastures was high locally, and low over larger spatial scales (vegetation type or biogeographical province). In all four vegetation types grazing was associated with differences in dung beetle community composition. Main conclusions The impact of grazing on dung beetle diversity is dependent to a considerable degree on the local ecological conditions and the biogeographical context that has shaped the composition of communities over time.

Coastal reclamation profoundly alters soil physicochemical conditions and strongly influences soil microbial ecology; however, the millennial-scale successional patterns and assembly mechanisms of prokaryotic communities under such long-term disturbance remain insufficiently understood. In this study, we investigated archaeal and bacterial communities in the plow layer along a 0–1000-year coastal reclamation chronosequence on the southern shore of Hangzhou Bay. We analyzed community abundance, diversity, composition and assembly processes, and quantified the relative contributions of geographic distance, environmental factors and reclamation years to microbial biogeographic patterns. The results showed that reclamation markedly drove continuous soil desalination, acidification, nutrient accumulation, and particle-size refinement. Bacterial abundance exhibited a sharp decline during the early stages of reclamation, whereas archaeal abundance remained relatively stable. The α-diversity of both archaea and bacteria peaked at approximately 210–230 years of reclamation. Community assembly processes differed substantially between the two microbial domains: the archaeal communities were dominated by stochastic processes (77.78%) identified as undominated processes and dispersal limitation, whereas bacterial communities were primarily shaped by deterministic processes (70.75%) driven as variable selection. Distance–decay analysis indicated that bacterial communities were more sensitive to environmental gradients. Multiple regression and variance partitioning further demonstrated that soil pH and electrical conductivity were the key drivers of community structure. Overall, this study reveals the millennial-scale community dynamics and assembly mechanisms of archaea and bacteria in response to coastal reclamation, providing mechanistic insights into long-term microbial ecological succession and offering valuable guidance for sustainable agricultural management and ecological restoration in reclaimed coastal regions.