The Relative Importance of Niche Process and Neutral Process in the Community Assembly of Subtropical Karst Forest: A Perspective on the Changes of Species Distribution Patterns at Different Scales

Background and aimsThe importance of niche processes and neutral processes to community assembly has been affirmed by most studies, although their relative importance needs to be determined in many systems. Moreover, as the spatial scale changes, the ecological processes that determine the community pattern may differ. We tested these ideas in subtropical karst forest in southwestern China in order to aid efforts of community reconstruction.MethodsTo test the importance of niche-based and neutral mechanisms we compared the fit six models to the observed SAD of the plot at three different sampling scales (10 m × 10 m, 20 m × 20 m, 50 m × 50 m). We also used spatial autocorrelation and distance-based Moran's eigenvector maps (dbMEM) combined with variation partitioning to further determine the relative contribution of the niche process and the neutral process under different sampling scales.ResultsThe neutral theoretical and statistical models fit the observed species abundance distribution curve best at each sampling scale. And variation partitioning showed that although the contribution of spatial structure was lower at larger sampling scales, it was still important, suggesting that neutral processes drive community structure at all sampling scales. In contrast, habitat filtering and interspecies competition may lead to a net weakening of the contribution of the niche process to the species abundance pattern of the community because they act in opposite directions. ConclusionsIn the restoration and reconstruction of local karst forest communities, environmental heterogeneity, inter-species relationships, and geographic spatial differences should all be considered.

Hummingbird abundance is related to food resources availability in a temperate forest of central Mexico

One strategy animals perform to cope scarcity of food resources is to shift in number of individuals according towards areas with available resources. This strategy can be more marked in species that are constrained by high energetic requirements such as hummingbirds. We aim to determine the extent to which the availability of food resources could be predictor of hummingbird numbers within and across hummingbird species in a temperate forest of central Mexico. We anticipate fluctuations in the number of hummingbirds grouped by species is best explained by monthly fluctuations in flowering resources species compared to pooled data. Our results indicate all seven hummingbird species fluctuate monthly in number across the year, which corresponds to monthly fluctuations of plant species they feed upon. The Basilinna leucotis and the Salvia elegans were present and interact in the study area almost all year-round, guiding the abundance pattern of both plants and hummingbirds in the study site. Generalized Linear Mixed Models indicate that although considering the abundance of the number of flowers for all plant species together could explain the fluctuation in all hummingbird species pooled together, considering both plant species and hummingbird species separately can provide a better explanation for changes in bird abundance. The model that analyzed species indicate that the interaction between the year-round species B. leucotis and S. elegans recorded the highest significant size effect. Our results highlight the fact that abundant species guiding abundance patterns could obscure by-species hummingbird trends and the processes guiding their patterns of abundance. We point out the need for performing adequate analytical approaches that can detect important biological interactions, and the likelihood of changes in habitat changing the pattern observed

Nitrogen evolution in the halo, thick disc, thin disc, and bulge of the Galaxy

ABSTRACT We study the evolution of nitrogen (N) in the Galactic halo, thick disc, thin disc, and bulge by comparing detailed chemical evolution models with recent observations. The models used in this work have already been constrained to explain the abundance patterns of α-elements and the metallicity distribution functions of halo, disc, and bulge stars; here, we adopt them to investigate the origin and evolution of N in the different Galactic components. First, we consider different sets of yields and study the importance of the various channels proposed for N production. Secondly, we apply the reference models to study the evolution of both the Galactic discs and bulge. We conclude that: i) primary N produced by rotating massive stars is required to reproduce the plateau in log(N/O) and [N/Fe] ratios at low metallicity, as well as the secondary and primary production from low- and intermediate-mass stars to reproduce the data of the thin disc; ii) the parallel model can provide a good explanation of the evolution of N abundance in the thick and thin discs, and we confirm that the thick disc has evolved much faster than the thin disc, in agreement with the results from the abundance patterns of other chemical elements; and iii) finally, we present new model predictions for N evolution in the Galactic bulge, and we show that the observations in bulge stars can be explained if massive stars rotate fast during the earliest phases of Galactic evolution, in agreement with findings from the abundance pattern of carbon.

The effect of microbial selection on the occurrence-abundance patterns of microbiomes

Theoretical models are useful to investigate the drivers of community dynamics. Notable are models that consider the events of death, birth, and immigration of individuals assuming they only depend on their abundance — thus, all types share the same parameters. The community level expectations arising from these simple models and their agreement to empirical data have been discussed extensively, often suggesting that in nature, rates might indeed be neutral or their differences not important. But, how robust are these model predictions to type-specific rates? And, what are the consequences at the level of types? Here, we address these questions moving from simple to diverse communities. For this, we build a model where types are differently adapted to the environment. We adapt a computational method from the literature to compute equilibrium distributions of the abundance. Then, we look into the occurrence-abundance pattern often reported in microbial communities. We observe that large immigration and biodiversity — common in microbial systems — lead to such patterns, regardless of whether the rates are neutral or non-neutral. We conclude by discussing the implications to interpret and test empirical data.

Evaluation of Three Prokaryote Primers for Identification of Prokaryote Community Structure and Their Abode Preference in Three Distinct Wetland Ecosystems

The ultimate role of prokaryote (bacteria and archaea), the decomposer of the wetland ecosystem, depends on its community structure and its interaction with the environment. The present study has used three universal prokaryote primers to compare prokaryote community structure and diversity of three distinctly different wetlands. The study results revealed that α-diversity indices and phylogenetic differential abundance patterns did not differ significantly among primers, but they did differ significantly across wetlands. Microbial community composition revealed a distinct pattern for each primer in each wetland. Overall comparison of prokaryote communities in sediments of three wetlands revealed the highest prokaryote richness and diversity in Bhomra (freshwater wetland) followed by Malencho (brackish-water wetland) and East Kolkata wetland (EKW) (sewage-fed wetland). Indicator genus analysis identified 21, 4, and 29 unique indicator genera, having preferential abode for Bhomra, EKW, and Malencho, respectively. Prediction of potential roles of these microbes revealed a preference for sulfate-reducing microbes in Malencho and methanogens in Bhomra. The distinct phylogenetic differential abundance pattern, microbial abode preference, and their potential functional role predict ecosystem variables shaping microbial diversity. The variation in community composition of prokaryotes in response to ecosystem variables can serve as the most sensitive bioindicator of wetland ecosystem assessment and management.

Phosphorus Availability Alters the Effect of Tree Girdling on the Diversity of Phosphorus Solubilizing Soil Bacterial Communities in Temperate Beech Forests

Phosphorus (P) solubilization is an important process for P acquisition by plants and soil microbes in most temperate forests. The abundance of inorganic P solubilizing bacteria (PSB) is affected by the P concentration in the soil and the carbon input by plants. We used a girdling approach to investigate the interplay of root-derived C and initial P content on the community composition of gcd-harboring bacteria as an example of PSB, which produce gluconic acid. We hypothesized that gcd-harboring PSB communities from P-poor sites are more vulnerable to girdling, because of their lower diversity, and that a shift in gcd-harboring PSB communities by girdling is caused by a response of few, mostly oligotrophic, taxa. We used a high-throughput metabarcoding approach targeting the gcd gene, which codes for the quinoprotein glucose dehydrogenase, an enzyme involved in the solubilization of inorganic P. We compared the diversity of gcd-harboring PSB in the mineral topsoil from two temperate beech forests with contrasting P stocks, where girdling was applied and compared our data to the respective control plots with untreated young beech trees. At both sites, gcd-harboring PSB were dominated by Proteobacteria and Acidobacteria, however, with differences in relative abundance pattern on the higher phylogenetic levels. The P-poor site was characterized by a high relative abundance of Kaistia, whereas at the P-rich site, Dongia dominated the gcd-harboring bacterial communities. Girdling induced an increase in the relative abundance of Kaistia at the P-poor site, whereas other bacterial groups of the family Rhizobiaceae were reduced. At the P-rich site, major microbial responders differed between treatments and mostly Bradyrhizobium and Burkholderia were positively affected by girdling in contrast to uncultured Acidobacteria, where reduced relative abundance was found. Overall, these effects were consistent at different time points analyzed after the introduction of girdling. Our data demonstrate that plant-derived carbon influences community structure of gcd-harboring bacteria in temperate beech forest soils.

The Metal Content of the Hot Atmospheres of Galaxy Groups

Galaxy groups host the majority of matter and more than half of all the galaxies in the Universe. Their hot (107 K), X-ray emitting intra-group medium (IGrM) reveals emission lines typical of many elements synthesized by stars and supernovae. Because their gravitational potentials are shallower than those of rich galaxy clusters, groups are ideal targets for studying, through X-ray observations , feedback effects, which leave important marks on their gas and metal contents. Here, we review the history and present status of the chemical abundances in the IGrM probed by X-ray spectroscopy. We discuss the limitations of our current knowledge, in particular due to uncertainties in the modeling of the Fe-L shell by plasma codes, and coverage of the volume beyond the central region. We further summarize the constraints on the abundance pattern at the group mass scale and the insight it provides to the history of chemical enrichment. Parallel to the observational efforts, we review the progress made by both cosmological hydrodynamical simulations and controlled high-resolution 3D simulations to reproduce the radial distribution of metals in the IGrM, the dependence on system mass from group to cluster scales, and the role of AGN and SN feedback in producing the observed phenomenology. Finally, we highlight future prospects in this field, where progress will be driven both by a much richer sample of X-ray emitting groups identified with eROSITA, and by a revolution in the study of X-ray spectra expected from micro-calorimeters onboard XRISM and ATHENA.

The composition of subduction zone fluids and the origin of the trace element enrichment in arc magmas

The partitioning of major and trace elements between eclogite and aqueous fluids with variable salinity was studied at 700–800 °C and 4–6 GPa in piston cylinder and multi anvil experiments. Fluid compositions were determined using the diamond trap technique combined with laser ablation ICP-MS measurements in the frozen state. In addition to NaCl, SiO2 is the main solute in the fluids. The fluid/eclogite partition coefficients of the large ion lithophile elements (LILE), such as Rb, Cs, Sr, and Ba as well as those of the light rare earths (LREE), of Pb, and of U increase by up to three orders of magnitude with salinity. These elements will therefore be efficiently transported by saline fluids. On the other hand, typical high field strength elements, such as Ti, Nb, and Ta, are not mobilized even at high salinities. Increasing temperature and pressure gradually increases the partitioning into the fluid. In particular, Th is mobilized by silica-rich fluids at 6 GPa already at low salinities. We show that we can fully reproduce the trace element enrichment pattern of primitive arc basalts by adding a few percent of saline fluid (with 5–10 wt% Cl) released from the basaltic slab to the zone of melting in the mantle wedge. Assuming 2 wt% of rutile in the eclogite equilibrated with the saline fluid produces a negative Nb Ta anomaly that is larger than in most primitive arc basalts. Therefore, we conclude that the rutile fraction in the subducted eclogite below most arcs is likely < 1 wt%. In fact, saline fluids would even produce a noticeable negative Nb Ta anomaly without any rutile in the eclogite residue. Metasomatism by sediment melts alone, on the other hand, is unable to produce the enrichment pattern seen in arc basalts. We, therefore, conclude that at least for primitive arc basalts, the release of hydrous fluids from the basaltic part of the subducted slab is the trigger for melting and the main agent of trace element enrichment. The contribution of sediment melts to the petrogenesis of these magmas is likely negligible. In the supplementary material, we provide a “Subduction Calculator” in Excel format, which allows the calculation of the trace element abundance pattern in primitive arc basalts as function of fluid salinity, the amount of fluid released from the basaltic part of the subducted slab, the fluid fraction added to the source, and the degree of melting.

Transcriptomic and proteomic analysis of putative digestive proteases in the salivary gland and gut of Empoasca (Matsumurasca) onukii Matsuda

Background Infestation by tea green leafhoppers (Empoasca (Matsumurasca) onukii) can cause a series of biochemical changes in tea leaves. As a typical cell-rupture feeder, E. onukii secretes proteases while using its stylet to probe the tender shoots of tea plants (Camellia sinensis). This study identified and analyzed proteases expressed specifically in the salivary gland (SG) and gut of E. onukii through enzymatic activity assays complemented with an integrated analysis of transcriptomic and proteomic data. Results In total, 129 contigs representing seven types of putative proteases were identified. Transcript abundance of digestive proteases and enzymatic activity assays showed that cathepsin B-like protease, cathepsin L-like protease, and serine proteases (trypsin- and chymotrypsin-like protease) were highly abundant in the gut but moderately abundant in the SG. The abundance pattern of digestive proteases in the SG and gut of E. onukii differed from that of other hemipterans, including Nilaparvata lugens, Laodelphax striatellus, Acyrthosiphum pisum, Halyomorpha halys and Nephotettix cincticeps. Phylogenetic analysis showed that aminopeptidase N-like proteins and serine proteases abundant in the SG or gut of hemipterans formed two distinct clusters. Conclusions Altogether, this study provides insightful information on the digestive system of E. onukii. Compared to five other hemipteran species, we observed different patterns of proteases abundant in the SG and gut of E. onukii. These results will be beneficial in understanding the interaction between tea plants and E. onukii.

Protein Binding Partners of Dysregulated miRNAs in Parkinson’s Disease Serum

Accumulating evidence suggests that microRNAs (miRNAs) are a contributing factor to neurodegenerative diseases. Although altered miRNA profiles in serum or plasma have been reported for several neurodegenerative diseases, little is known about the interaction between dysregulated miRNAs and their protein binding partners. We found significant alterations of the miRNA abundance pattern in serum and in isolated serum-derived extracellular vesicles of Parkinson’s disease (PD) patients. The differential expression of miRNA in PD patients was more robust in serum than in isolated extracellular vesicles and could separate PD patients from healthy controls in an unsupervised approach to a high degree. We identified a novel protein interaction partner for the strongly dysregulated hsa-mir-4745-5p. Our study provides further evidence for the involvement of miRNAs and HNF4a in PD. The demonstration that miRNA-protein binding might mediate the pathologic effects of HNF4a both by direct binding to it and by binding to proteins regulated by it suggests a complex role for miRNAs in pathology beyond the dysregulation of transcription.