Niche Process Research Articles

Accounting for the microbial assembly of each process in wastewater treatment plants (WWTPs): study of four WWTPs receiving similar influent streams.

We evaluated a unique model in which four full-scale wastewater treatment plants (WWTPs) with the same treatment schematic and fed with similar influent wastewater were tracked over an 8-month period to determine whether the community assembly would differ in the activated sludge (AS) and sand filtration (SF) stages. For each WWTP, AS and SF achieved an average of 1-log10 (90%) and <0.02-log10 (5%) reduction of total cells, respectively. Despite the removal of cells, both AS and SF had a higher alpha and beta diversity compared to the influent microbial community. Using the Sloan neutral model, it was observed that AS and SF were individually dominated by different assembly processes. Specifically, microorganisms from influent to AS were predominantly determined by the selective niche process for all WWTPs, while the microbial community in the SF was relatively favored by a stochastic, random migration process, except two WWTPs. AS also contributed more to the final effluent microbial community compared with the SF. Given that each WWTP operates the AS independently and that there is a niche selection process driven mainly by the chemical oxygen demand concentration, operational taxonomic units unique to each of the WWTPs were also identified. The findings from this study indicate that each WWTP has its distinct microbial signature and could be used for source-tracking purposes.IMPORTANCEThis study provided a novel concept that microorganisms follow a niche assembly in the activated sludge (AS) tank and that the AS contributed more than the sand filtration process toward the final microbial signature that is unique to each treatment plant. This observation highlights the importance of understanding the microbial community selected by the AS stage, which could contribute toward source-tracking the effluent from different wastewater treatment plants.

Plant community assembly of alpine meadow at different altitudes in NortheastQinghai‐TibetPlateau

AbstractThe mechanism of community assembly is the core of ecological research. Using phylogenetic‐based and functional trait‐based methods jointly to explore the processes is a useful way to explain the change in assembly mechanisms. The present study combined these methods to explore the mechanism of plant community assembly in alpine meadows at different altitudes on the northeast Qinghai‐Tibet Plateau. We established a permanent study plot of 1.85 × 105 m2and investigated 162 quadrats of 50 × 50 cm. We calculated the species richness, phylogenetic diversity (PD), standardized effect sizes PD (SES·PD), mean pairwise distance (SES·MPD), mean nearest taxon distance (SES·MNTD), and analyzed plant functional traits and phylogenetic signals. We found that the species richness and PD of plant community showed a “hump‐shaped” pattern, SES·PD showed a decreasing trend, and the phylogenetic structure changed from overdispersion (SES·MPD &gt; 0, SES·MNTD &gt; 0) to clustering (SES·MPD &lt; 0, SES·MNTD &lt; 0) with increasing altitude. The functional structure changed from overdispersion (nearest function index [NFI] &lt; 0) to clustering (NFI &gt; 0) with increasing altitude. Specific leaf area, leaf carbon content, and leaf phosphorus content had weak phylogenetic signals (K &lt; 1,p &lt; 0.05), and the other functional traits (plant height, leaf nitrogen content, leaf dry matter content, and relative chlorophyll content) did not show phylogenetic signals (K &lt; 1,p &gt; 0.05). The above results showed that competitive exclusion was the main driving force of community assembly at low altitudes (3000 and 3250 m), and habitat filtration was the main driving force of community assembly at high altitudes (4000 and 4500 m). For medium altitudes (3500 and 3750 m), the habitat was more complex because it was in the transition area between high and low altitudes, so the process of community construction may be random, habitat filtering, or competitive exclusion. On the whole, the niche process (deterministic process) was more important in driving for plant community assembly in the alpine meadow of the Qinghai‐Tibetan Plateau.

Survey on the Advantages of Metal 3D Printing Using Laser Sintering Compared to Traditional Metal Manufacturing Methods

AbstractAdditive manufacturing (AM) is a niche process that has seen extensive growth and adoption in the past decade in the industrial sector. Among the AM techniques present on the market today there are identified only a few methods allowing the 3D printing of metallic materials to be of special interest for their applications in various domains like the automotive, aeronautical, and healthcare industries. The most important questions needing answers are how to produce components from metallic materials that have superior qualities like versatility, wear resistance, ease of customization, and ease of integration with existing components. Compared to traditional metalworking methods where it has been studied how the metal behaves and morphs during the process and where it is known exactly what to do in order to modify the properties of the resulting component into a favor metal, AM changes everything, forcing a researcher to start from the beginning. While the technology is starting to be used more and more, the need to find production methods leads to consistent quality products and with outstanding material properties. New methods need to be developed to help attune the properties of the 3D printed parts to the requirements of their respective uses. The present study refers to 3D metal additive manufacturing (MAM), providing an overview on the process itself and its possible results as well as hurdles with added methods to overcome them.

The effects of long-term warming on arbuscular mycorrhizal fungal communities depend on habitat type on the Qinghai-Tibet Plateau

Arbuscular mycorrhizal fungi (AMF) are widespread root-associated microorganisms that participate in many ecosystem processes. However, the response of AMF communities to global warming still remains poorly understood, especially in high-altitude regions. This study investigated the responses of AMF communities to 17-year experimental warming with open top chambers in two habitat types (i.e., shrubland and meadow) of the alpine meadow ecosystem of the Qinghai–Tibet Plateau. For this, 454-pyrosequencing was used and the main ecological processes that structure AMF communities were inferred based on distributions of species abundance and phylogenetic patterns. A total of 110 different AMF phylotypes (shrubland habitat: 102; meadow habitat: 91) were identified in both habitats, predominantly belonging to Glomeraceae. Eighty AMF phylotypes were found in both habitats, and phylotypes affiliated with Acaulosporaceae and Archaeosporaceae were only found in the shrubland habitat. Warming did not affect AMF diversity or community composition in the shrubland habitat; however, in the meadow habitat, warming caused a decline of AMF species richness by 45.6%. Moreover, the taxon composition of AMF communities was changed via the negative influence of root biomass in the meadow habitat. Mandelbrot, based on the niche process, was the best-fitting model for all fungal data sets in both habitats, indicating that fungal community dynamics under warming treatments matched niche-based processes in both habitats. Moreover, the phylogenetic structure of AMF communities was always phylogenetically clustered regardless of warming in the shrubland habitat. However, the phylogenetic structure changed from phylogenetic clustering of the control treatment to random of warming treatment in the meadow habitat. This suggests that in the shrubland habitat, warming does not change the central ecological process that structures AMF communities, but rather, leads to the transformation of the central process from environmental filtration to the neutralization of habitat filtration and competition exclusion in the meadow habitat. In summary, these results indicate that the effect of long-term warming on the assemblage of AMF communities depends on the habitat type. This illustrates that maintaining a high habitat type complexity is conducive for the response of alpine meadow ecosystems to climate warming.

Species-abundance distribution patterns of Quercus aliena var. acutiserrata forest in Taibai Mountain, China.

The statistical model (log-normal model), niche models (Zipf model, broken stick mo-del, niche preemption model), and neutral model were used to fit the species-abundance distribution patterns based on the measurements of environmental factors and inventory data of trees with DBH≥1 cm in a 1.5 hm2 plot in the primary forest (PF) and a 1.5 hm2 plot in the secondary forest (SF). The results showed that species-abundance distribution was affected by habitat heterogeneity in Q. aliena var. acutiserrata forest. Topography had a predominant impact on the species-abundance distribution in PF. Species distribution was affected by both neutral and niche processes, with neutral process having a less prominent effect in large convexity habitats. While the neutral model was rejected by the K-S and Chi-square test in low convexity habitats, the species-abundance distribution satisfied the assumption of niche theory. Niche process and neutral process were equally important in the community in areas with steep slopes, while niche differentiation was the dominant in flat areas. In SF, the main factors affecting species distribution were soil nutrients. The niche process was the mainly ecological process affected species-abundance distribution in habitats with high soil available phosphorus, while the niche and neutral processes existed simultaneously in habitats with low soil phosphorus availability. There was a significant scale effect on the species-abundance distribution pattern of Q. aliena var. acutiserrata forests in Taibai Mountain. The niche and neutral processes could protect the species-abundance distribution at the 20 m×20 m scale in PF, while the niche process could explain the species-abundance distribution at the 40 m×40 m and 70 m×70 m scales. The niche and neutral processes combined acted on the species abundance distribution at the 20 m×20 m, 40 m×40 m and 70 m×70 m scales in SF, with niche process being more important than neutral process. Moreover, besides the scale and habitat heterogeneity, the species-abundance distribution patterns of Q. aliena var. acutiserrata forests differed significantly between primary forest and secondary forest under anthropogenic disturbance.

Tropical rainforest conversion into rubber plantations results in changes in soil fungal composition, but underling mechanisms of community assembly remain unchanged

Fungi play an important role in maintaining tropical forest diversity. However, little research to date has examined the effects of forest conversion (from rainforest to rubber plantation) on fungal community composition and diversity. In this study, we used Illumina MiSeq sequencing to assess soil fungal community composition and diversity for both rubber plantations and rainforest. We found: (1) Distinct differences in soil fungal community composition between rainforest and rubber plantation sites, indicating an important effect of forest conversion. The Ascomycota (36.71%) was the most abundant phylum in the rubber plantations, followed by the Basidiomycota (12.43%); these two phyla reversed in abundance in the tropical rainforest. (2) The OTU richness and Faith’s phylogenetic diversity were comparable in the plantations and rainforest, suggesting that conversion did not result in a reduction in α diversity. However, conversion resulted in a reduction in β diversity and a net loss of total diversity. (3) Community similarity of rubber plantations and rainforests declined with the distance among sample points at the fine scale, suggesting that dispersal limitation (a neutral process) was the main mechanism of fungal community assembly. Spatial variables (i.e., site location and elevation) accounted for 28% of the total variance in diversity, and therefore habitat filtering (a niche process) may drive fungal community assembly at the regional scale. In conclusion, the conversion of tropical rainforest to rubber plantations altered the composition of soil fungal communities, and reduced β diversity which resulted in a net loss of landscape level diversity. However, the underling mechanisms of community assembly remain unchanged. Neutral processes may explain fungal community assembly at fine scales, whereas niche processes likely drive patterns of assembly at the regional scale.

Macroporous heparin-based microcarriers allow long-term 3D culture and differentiation of neural precursor cells

Adult neurogenesis and the neurogenic niche in the dentate gyrus are subjects of much research interest. Enhancing our knowledge of this niche process and the role played by this unique microenvironment would further our understanding of plasticity and its relevance for cognition in health and disease. The complex three-dimensional (3D) nature of the niche microenvironment is poorly recapitulated in current cell culture experimental procedures. Neural precursor cells (NPCs) are cultured either on two-dimensional (2D) surfaces, where cells quickly reach confluency and passaging is required, or as 3D neurospheres, with the limitation of poor diffusion of nutrients and thus partial differentiation of cells over time. Herein, we culture NPCs on microscale scaffolds termed microcarriers, composed of poly(ethylene glycol) and heparin, designed to more closely represent the 3D environment of the neurogenic niche. The interconnected macroporous structure of the microcarriers allows NPCs to attach to their pore walls with subsequent continuous proliferation (analyzed up to 28 days) without formation of a necrotic core. Removal of basic fibroblast growth factor and epidermal growth factor from the culture medium results in differentiation of the NPCs. Unlike 2D culture, a high percentage of neurons was achieved on the microcarriers (22% MAP2 positive cells) indicating that these 3D microscale scaffolds give a more conducive environment for neuronal differentiation. Microcarrier culture of NPCs allows long-term cell expansion and better differentiation, which provides superior culture conditions for studying/modelling the neurogenic niche.

Relative roles of niche and neutral processes on turnover of plant, fungal and bacterial communities in arid and semi-arid areas at the regional scale

The mechanisms that determine the spatial structure of macroscopic and microbial communities and how they respond to environmental changes are central themes that have been explored in ecological research. However, little is known about the relative roles and importance of neutral and niche-related factors in the assemblage of bacterial, fungal, and plant communities. Here partial Mantel, null model, and variation partitioning analysis were used to compare mechanisms driving the beta diversity of bacteria, fungi and plant communities at the regional scale in arid and semi-arid areas. Denaturing gradient gel electrophoresis (PCR-DGGE) was used to evaluate the distribution pattern of microbial communities, and vegetation survey were conducted to evaluate the characteristics of plant communities. We found that bacterial, fungal, and plant communities were strongly influenced by niche processes at the regional scale in arid and semi-arid areas. Bacteria had a stronger habitat association, indicating community assembly is strongly affected by niche processes. Fungi, with their body size between plants and bacteria, had moderate environment correlation, and plants had less environment association than fungi or bacteria, which suggests that body size may determine the association between organism and environment. We concluded that the pivotal niche process, environmental filtering, weakened with increasing body size, and it should be considered when we evaluate the relative roles of deterministic and stochastic processes in community assemblage.

Machine Shops go Deep

Steed Webzell reports on recent deep hole drilling projects for subcontractors, as well as the initiative of a product manufacturer to bring this niche process in house

Assessing the Hybrid Effects of Neutral and Niche Processes on Gut Microbiome Influenced by HIV Infection.

That both stochastic neutral and deterministic niche forces are in effect in shaping the community assembly and diversity maintenance is becoming an increasingly important consensus. However, assessing the effects of disease on the balance between the two forces in the human microbiome has not been explored to the best of our knowledge. In this article, we applied a hybrid model to address this issue by analyzing the potential effect of HIV infection on the human gut microbiome and adopted a further step of multimodality testing to improve the interpretation of their model. Our study revealed that although niche process is the dominant force in shaping human gut microbial communities, niche process- and neutral process-driven taxa could coexist in the same microbiome, confirming the notion of their joint responsibility. However, we failed to detect the effect of HIV infection in changing the balance. This suggests that the rule governing community assembly and diversity maintenance may be changed by the disturbance from HIV infection-caused dysbiosis. Although we admit that the general question of disease effect on community assembly and diversity maintenance may still be an open question, our study presents the first piece of evidence to reject the significant influence of diseases.

Trait-Environment Relationship of Aquatic Vegetation in a Tropical Pond Complex System

The relationship between organisms’ traits and the characteristics of their habitats has been a central theme in ecology. Using two complementary approaches to analyze three-matrices of species composition, functional trait, and environment data (RLQ and fourth-corner analyses), we tested if environmental gradient determines aquatic plant traits in ponds in the Pantanal wetland. Furthermore, we tried to understand if plant composition is spatially structured and if environmental gradient is correlated with taxonomic and functional community properties. We sampled aquatic plants coverage in 20 ponds and measured pond size, depth and pH to represent the environmental gradient. We found significant turnover of several traits of aquatic plants along the environmental gradient, being niche partitioning the most probable process structuring plant communities. There was no evidence of spatial autocorrelation determining species composition in the scale of the study, which may indicate that the annual flooding can act as homogenizing factor that promotes species co-occurrence along the ponds. Taxonomic abundance and functional richness were positively related with environmental gradient. Larger and deeper ponds provide higher resource availability thus supporting more functional attributes and vegetation cover. Our results support the hypothesis that niche process is the main driver of aquatic plants in the Pantanal.

Responses of species abundance distribution patterns to spatial scaling in subtropical secondary forests.

To quantify and assess the processes underlying community assembly and driving tree species abundance distributions(SADs) with spatial scale variation in two typical subtropical secondary forests in Dashanchong state‐owned forest farm, two 1‐ha permanent study plots (100‐m × 100‐m) were established. We selected four diversity indices including species richness, Shannon–Wiener, Simpson and Pielou, and relative importance values to quantify community assembly and biodiversity. Empirical cumulative distribution and species accumulation curves were utilized to describe the SADs of two forests communities trees. Three types of models, including statistic model (lognormal and logseries model), niche model (broken‐stick, niche preemption, and Zipf‐Mandelbrodt model), and neutral theory model, were estimated by the fitted SADs. Simulation effects were tested by Akaike's information criterion (AIC) and Kolmogorov–Smirnov test. Results found that the Fagaceae and Anacardiaceae families were their respective dominance family in the evergreen broad‐leaved and deciduous mixed communities. According to original data and random sampling predictions, the SADs were hump‐shaped for intermediate abundance classes, peaking between 8 and 32 in the evergreen broad‐leaved community, but this maximum increased with size of total sampled area size in the deciduous mixed community. All niche models could only explain SADs patterns at smaller spatial scales. However, both the neutral theory and purely statistical models were suitable for explaining the SADs for secondary forest communities when the sampling plot exceeded 40 m. The results showed the SADs indicated a clear directional trend toward convergence and similar predominating ecological processes in two typical subtropical secondary forests. The neutral process gradually replaced the niche process in importance and become the main mechanism for determining SADs of forest trees as the sampling scale expanded. Thus, we can preliminarily conclude that neutral processes had a major effect on biodiversity patterns in these two subtropical secondary forests but exclude possible contributions of other processes.

Effects of Topography on Tree Community Structure in a Deciduous Broad-Leaved Forest in North-Central China

Topography strongly influences the compositional structure of tree communities and plays a fundamental role in classifying habitats. Here, data of topography and 16 dominant tree species abundance were collected in a fully mapped 25-ha forest plot in the Qinling Mountains of north-central China. Multivariate regression trees (MRT) were used to categorize the habitats, and habitat associations were examined using the torus-translation test. The relative contributions of topographic and spatial variables to the total community structure were also examined by variation partitioning. The results showed the inconsistency in association of species with habitats across life stages with a few exceptions. Topographic variables [a + b] explained 11% and 19% of total variance at adult and juvenile stage, respectively. In contrast, spatial factors alone [c] explained more variation than topographic factors, revealing strong seed dispersal limitation in species composition in the 25-ha forest plot. Thus, the inconsistent associations of species and habitats coupled with high portion of variation of species composition explained by topographic and spatial factors might suggest that niche process and dispersal limitation had potential influences on species assemblage in the deciduous broad-leaved forest in north-central China.

Host Phylogeny Is a Major Determinant of Fagaceae-Associated Ectomycorrhizal Fungal Community Assembly at a Regional Scale.

Environmental filtering (niche process) and dispersal limitation (neutral process) are two of the primary forces driving community assembly in ecosystems, but how these processes affect the Fagaceae-associated ectomycorrhizal (EM) fungal community at regional scales is so far poorly documented. We examined the EM fungal communities of 61 plant species in six genera belonging to the Fagaceae distributed across Chinese forest ecosystems (geographic distance up to ∼3,757 km) using Illumina Miseq sequencing of ITS2 sequences. The relative effects of environmental filtering (e.g., host plant phylogeny, soil and climate) and dispersal limitation (e.g., spatial distance) on the EM fungal community were distinguished using multiple models. In total, 2,706 operational taxonomic units (OTUs) of EM fungi, corresponding to 54 fungal lineages, were recovered at a 97% sequence similarity level. The EM fungal OTU richness was significantly affected by soil pH and nutrients and by host phylogeny. The EM fungal community composition was significantly influenced by combinations of host phylogeny, spatial distance, soil and climate. Furthermore, host phylogeny had the greatest effect on EM fungal community. The study suggests that the assembly of the EM fungal community is governed by both environmental filtering and dispersal limitation, with host effect being the most important determinant at the regional scale.

SOLUTION-DIFFUSION MODEL FOR A SMALL SCALE REVERSE OSMOSIS SYSTEM

Reverse osmosis (RO) often used for desalination, in producing the ultrapure water for electronics, pharmaceuticals and power generation industries and also it was used in small niche process such as food processing and pollution control. Analysis of membrane performance required multiple of experimental run. Experimental work can be time consuming and costly. Hence, this work aims to model a small scale RO system by using a solution-diffusion model to minimize the experimental work. The model was verified by comparing the data obtained from the model and experimental data. Other studies, which include, the influence of solute feed concentration on the RO system was also been investigated. A commercial RO Trisep flat sheet membrane was used. The solute permeate concentrations, solvent permeate flux, final solute feed concentrations and rejection rate of sodium chloride (NaCl) was analyzed to observe the membrane performance. Result shows that some experimental data has almost similar trend with the simulated data. Both solute feed concentration and rejection rate of NaCl over time show almost similar trends with percentage errors are 8.89% and 0.76% respectively. As solute feed concentration increased, the solute permeate concentration increased. In contrast to the solute permeate concentration, when the solute feed increases the solvent permeate flux decreases and rejection rate will also decrease.

Diversity maintenance mechanism changes with vegetation type and the community size in a tropical nature reserve

AbstractSpecies‐abundance distribution (SAD) is an essential tool to explain the mechanism of diversity maintenance in ecological communities. Most of the studies on diversity maintenance in a specific forest dynamics plot just consider stems with a certain minimum size class to include into the tree community to be examined. However, the species in the juvenile stage are easily disturbed by a variety of factors; here, we define the minimum stem size to tag trees in a community as the community size (DBHmintag), which implies that the communities with different minimum diameter at breast height (DBH) sizes to tag trees are tree assemblages containing tree populations of different minimum DBH. We used data from 17 1‐ha forest dynamics plots across six old‐growth forest types in a tropical nature reserve to explore diversity maintenance mechanism by SAD curves (at three levels of DBHmintag) fitting to neutral model and niche preemption model. We found that the SADs of the two zonal vegetation types (tropical montane rain forest and tropical lowland rain forest) were best fitted by neutral model at each level of DBHmintag; meanwhile, the best fitted models for the four azonal vegetation types (tropical coniferous forest, tropical deciduous monsoon rain forest, tropical montane evergreen forest, and tropical montane dwarf forest) varied with DBHmintag levels, for communities with DBHmintag ≥ 1 cm and DBHmintag ≥ 5 cm, the fitting effect of neutral model was better than niche preemption model's for the forest dynamics plots in the four azonal vegetation types, and for communities with DBHmintag ≥ 10 cm, the four azonal vegetation types were all best fitted by the niche model. Our results suggest that species diversity maintenance mechanisms of the two zonal vegetation types derived from the neutral model increased the predictive accuracy at each level of DBHmintag, and meanwhile, the four azonal vegetation types derived from the neutral model increased the predictive accuracy at smaller community size; however, with the increase in DBHmintag, these communities derived from the niche theory model increased the predictive accuracy. Habitat heterogeneity might be the major constraints in determining the neutral or niche process for diversity maintenance of a specific forest community.

The importance of neutral and niche processes for bacterial community assembly differs between habitat generalists and specialists.

The mechanisms of community assembly are a central focus in the field of microbial ecology. However, to what extent these mechanisms differ in importance by traits of groups is poorly understood. Here we quantified the importance of neutral and niche processes in community assembly for bacteria, habitat specialists and generalists in 21 plateau lakes of China. Results showed that both neutral and niche processes played a critical role in the assembly of entire bacterial communities, shaping a unique biogeographical pattern. A few habitat generalists and many specialists were identified. Interestingly, habitat specialists were only governed by niche process, with seven significant environmental variables-salinity, dissolved oxygen, water transparency, total phosphorus, ammonium-nitrogen, temperature and total nitrogen-independently explaining 40.3% of the biological variation. By contrast, habitat generalists were strongly driven by neutral process, with 50.9% of the variation of detection frequency explained in neutral community model. Only three environmental variables-salinity, total nitrogen and dissolved oxygen-significantly affected the distribution of habitat generalists, independently explaining 13.6% of the variation. Governed by different assembly mechanisms, habitat specialists and generalists presented disparate biogeographical patterns. Our result emphasizes the importance of investigating the bacterial community assembly at more refined levels than entire communities.

Genomic and metagenomic surveys of hydrogenase distribution indicate H2 is a widely utilised energy source for microbial growth and survival.

Recent physiological and ecological studies have challenged the long-held belief that microbial metabolism of molecular hydrogen (H2) is a niche process. To gain a broader insight into the importance of microbial H2 metabolism, we comprehensively surveyed the genomic and metagenomic distribution of hydrogenases, the reversible enzymes that catalyse the oxidation and evolution of H2. The protein sequences of 3286 non-redundant putative hydrogenases were curated from publicly available databases. These metalloenzymes were classified into multiple groups based on (1) amino acid sequence phylogeny, (2) metal-binding motifs, (3) predicted genetic organisation and (4) reported biochemical characteristics. Four groups (22 subgroups) of [NiFe]-hydrogenase, three groups (6 subtypes) of [FeFe]-hydrogenases and a small group of [Fe]-hydrogenases were identified. We predict that this hydrogenase diversity supports H2-based respiration, fermentation and carbon fixation processes in both oxic and anoxic environments, in addition to various H2-sensing, electron-bifurcation and energy-conversion mechanisms. Hydrogenase-encoding genes were identified in 51 bacterial and archaeal phyla, suggesting strong pressure for both vertical and lateral acquisition. Furthermore, hydrogenase genes could be recovered from diverse terrestrial, aquatic and host-associated metagenomes in varying proportions, indicating a broad ecological distribution and utilisation. Oxygen content (pO2) appears to be a central factor driving the phylum- and ecosystem-level distribution of these genes. In addition to compounding evidence that H2 was the first electron donor for life, our analysis suggests that the great diversification of hydrogenases has enabled H2 metabolism to sustain the growth or survival of microorganisms in a wide range of ecosystems to the present day. This work also provides a comprehensive expanded system for classifying hydrogenases and identifies new prospects for investigating H2 metabolism.

Niche and Neutral Processes Together Determine Diversity Loss in Response to Fertilization in an Alpine Meadow Community

Fertilization via nutrient deposition and agricultural inputs is one of the most important factors driving decreases in plant diversity. However, we still do not fully understand which processes (niche process or neutral process) are more important in leading to decreases in plant diversity caused by fertilization. A hypothesis-based approach was used to test the relative importance of niche versus neutral processes along a fertilization gradient in an alpine meadow community on the eastern Tibetan plateau, China. Niche overlap values were calculated for species biomass, and the null model was used to generate the values of niche overlap expected at random. A linear regression modeling was used to evaluate the relationship between functional traits (specific leaf area, leaf dry matter content, and leaf total nitrogen concentration) and species relative abundance. Our results demonstrated that observed niche overlap for species biomass was significantly higher than expected at lower fertilization gradients. Moreover, we also found a significantly negative correlation between species relative abundance and specific leaf area and leaf dry matter content, but a significantly positive correlation between relative abundance and leaf nitrogen concentration at lower fertilization gradients. However, these relationships were not significant at higher fertilization gradients. We concluded that community assembly is dynamic progression along the environmental gradients, and niche and neutral processes may together determine species diversity loss in response to fertilization.

In vitro generation and characterization of chicken long-term germ cells from different embryonic origins

Primordial germ cells (PGCs) are the precursors of differentiated germ cells. Located in the epiblast of a stage X (EG&K) embryo, the PGCs translocate anteriorly to the germinal crescent and migrate, within 48 to 56 hours of development, through the blood vascular system to the germinal ridges where they become the gonadal germ cells (GGCs). We aim to generate, compare, and determine the basic characters of the in vitro long-term cultured PGCs derived from (1) the chicken blastodermal cells (at stages IX–XII); (2) the chicken blood of a 2-day old embryo (stages 14–17 Hamburger Hamilton [HH]); and (3) the long-term cultured gonocytes taken from male gonads of a 5- to 6-day-old embryo (stages 29–30 HH). In presence of fibroblast growth factor, chicken blastodermal cells are able to long-term proliferate and generate small, round, alkaline phosphatase–positive cell clusters. Molecular characterization shows that these selected and amplified clusters show a PGC-like cell profile, as they express cPOUV (a pluripotent-associated marker), NR6A1/GCNF and DDX4/CVH (germ cell–specific genes). Both chicken PGCs and GGCs, obtained from embryonic blood and gonads, at 14 to 17 HH and 29 to 30 HH, respectively, generate long-term germ cell cultures and positively react in vitro to periodic acid–Schiff. Immunochemical analyses reveal that these cell lines are specifically recognized by anti-SSEA-1, anti-EMA-1, anti-CVH, anti-β1-integrin, and anti-CEACAM antibodies. The presence of surrounding cells may suggest a stronger dependency toward the niche process for the GGCs. The reactivity of chicken embryonic germ cells obtained from the two different sources to the specific markers used in this study was not altered through the culture. In conclusion, the morphologic analysis specific for chicken PGCs and GGCs will further contribute to quick and reliable characterization of long-term cultured in vitro chicken germ cells.