Asynchronous patterns in soil bacterial diversity and functional potentials along an alpine altitudinal gradient.

The Qinghai-Tibet Plateau has experienced an increase in N deposition/input due to global change. However, it remains unclear how the responses and whether the responses of soil bacterial diversity to short-term N input are consistent at different levels. Here, we investigated soil bacterial species and phylogenetic α-diversity and community composition based on a short-term nitrogen input experiment (five levels: 0, 2.5, 5, 10, and 20 g N m−2 y−1) in an alpine steppe at the source of Brahmaputra, using high-throughput sequencing technology. Short-term nitrogen input did not affect the species α-diversity and β-diversity of soil bacteria. However, soil bacterial phylogenetic α-diversity and dissimilarity increased with increasing nitrogen input. Different relative contributions and correlations of primary factors to species and phylogenetic diversity under short-term nitrogen input may result in different responses, in which ecological processes also play a role. Therefore, studying the response of soil bacteria to short-term nitrogen input should take into account not only the species level but also the phylogenetic level. We should pay close attention to the potential influence of short-term nitrogen deposition/fertilization on the soil bacterial community in the alpine steppe on the Tibetan Plateau.

Understanding the mechanisms that influence the assembly of natural communities has become a central issue in ecological studies, especially because of the influence of diversity on ecosystem functioning. These mechanisms may be related to niche and neutral processes. Niche-related processes include selection imposed by the abiotic environment and biotic interactions, whereas neutral effects are related to chance or historical events. Mountain ecosystems are among the most suitable models for unraveling the interactions between the facets of biodiversity. The overall aim of this project was to understand the assembly processes of alpine and forest plant communities through phylogenetic and functional diversity across altitudinal gradients in tropical mountains. To respond to this approach, we selected areas from several tropical mountains worldwide. We used lists with altitude records from three tropical montane mountains of tropical ecosystems: Mount Puracé, Colombia; Mount Kilimanjaro, Tanzania; and Mount Haleakalā, Hawaii, USA (CAP. 1). In addition, six sampling sites were established along an elevation gradient of (3200-4100 m). At each station, 10 plots measuring 2.5 m x 4 m were established (CAP. 2 and 3). In addition, 28 isolated individuals of Espeletia lopezii (Asteraceae) were selected; a 70 cm diameter metal ring was centered on each caulescent rosette. In addition, 28 rings were established in the open areas (control) (CAP. 4). The alpha taxonomic diversity was estimated using Hill's numbers (q=0, q=1, q=2) (CAP. 2 and 4). For phylogenetic diversity, six phylogenetic metrics were calculated: lineage diversity as the total length of the phylogenetic branch (PD), mean pairwise phylogenetic distance (MPD), mean nearest taxon phylogenetic distance (MNTD), and standardized effect size of these metrics (CAP. 1, 2 and 4). To determine the functional responses that drive the assembly of communities along the elevation gradient, five functional traits were measured: leaf area, leaf length, leaf thickness, leaf dry matter content, and maximum plant height. The weighted community mean (CWM) of the traits and functional diversity (FD) were estimated (CAP. 3). Different statistical models were used to test the main effects of altitude and soil depth on taxonomic, phylogenetic, and functional metrics. In the three tropical mountains, an environmental filtering effect was observed with increasing altitude, causing phylogenetic clustering, decreasing phylogenetic diversity, and decreasing species richness. The decreasing phylogenetic distances between close relatives are congruent with neo-endemism, suggesting recent diversification of plants at high altitudes in tropical mountains, possibly driven by geographical isolation and environmental heterogeneity (CAP. 1). In Chapter 2, the results showed that as soil depth decreased and altitude increased, páramo plant communities showed a general pattern of decreasing phylogenetic diversity. These results are consistent with the general expectation that community assemblage attributes become more closely related as stressful environmental conditions increase along a gradient. In Chapter 3, the results showed that several functional traits (CWM) and several indices of functional diversity varied significantly along the altitude and soil gradient in the area. Three of the five functional traits showed the potential to describe how the functional composition of páramo communities responded to increasing environmental severity along these environmental gradients. The two functional diversity indices, FDis and FRic, significantly decreased with increasing elevation and decreasing soil depth. In Chapter 4, the vegetation under the canopy of the facilitator plants (E. lopezii) was found to have a positive impact on taxonomic diversity, compared to the control areas. Regarding phylogenetic diversity, the dominant pattern observed was mainly random. These results suggest that, at these altitudes, the metacommunity is strongly filtered by climatic and edaphic factors, and despite the benefits of the facilitation exerted by stem rosettes, it is difficult to detect a pattern of phylogenetic overdispersion. In Chapter 5, as a general trend, a greater number of species were found in locations at higher altitudes, decreasing in locations at lower altitudes, and where climatic seasonality is more marked and filters out species from lineages that are less tolerant to stressful environments. Nitrogen-fixing Fabaceae species were prominent among the important species, especially at low altitudes and more stressful sites. Keywords: Tropical mountains, altitudinal gradient, phylogenetic diversity, functional diversity, plant-plant interaction, community assembly.

Bacterial community composition is shaped by soil secondary salinization and acidification brought on by high nitrogen fertilization rates

Despite decades of interest, few studies have provided evidence supporting theoretical expectations for coupled relationships between aboveground and belowground diversity and ecosystem functioning in non-manipulated natural ecosystems. We characterized plant species richness and density, soil bacterial, fungal and eukaryotic species richness and phylogenetic diversity (using 16S, ITS, and 18S gene sequencing), and ecosystem function (levels of soil C and N, and rates of microbial enzyme activities) along a natural gradient in plant richness and density in high-elevation, C-deficient soils to examine the coupling between above- and belowground systems. Overall, we observed a strong positive relationship between aboveground (plant richness and density) and belowground (bacteria, fungi, and non-fungal eukaryotes) richness. In addition to the correlations between plants and soil communities, C and N pools, and rates of enzyme activities increased as plant and soil communities became richer and more diverse. Our results suggest that the theoretically expected positive correlation between above- and belowground communities does exist in natural systems, but may be undetectable in late successional ecosystems due to the buildup of legacy organic matter that results in extremely complex belowground communities. In contrast, microbial communities in early successional systems, such as the system described here, are more directly dependent on contemporary inputs from plants and therefore are strongly correlated with plant diversity and density.

From town to town: Predicting the taxonomic, functional and phylogenetic diversity of birds using NDVI

Studies in humans and livestock have demonstrated Bacillus coagulans GBI-30, 6086 to have probiotic potential, suggesting that it may alleviate gastrointestinal (GI) distress commonly associated with diet change in dogs. This study aimed to evaluate the effects of B. coagulans GBI-30, 6086 on fecal scores, pH, dry matter (DM) percentage, and microbiota populations of dogs following an abrupt diet change. English Pointer dogs (n = 12; age = 5.9 ± 2.5 yr; body weight = 26.6 ± 6.1 kg) were used in a replicated 3 × 3 Latin square design and fed commercial diets containing no probiotics or prebiotics. The following treatments were administered orally in gelatin capsules before each daily feeding: (1) placebo control (250 mg maltodextrin/day); (2) B. coagulans [low dose; 5 × 108 colony-forming units (CFU)/day]; and (3) B. coagulans (high dose; 2.5 × 109 CFU/day). An extruded kibble diet was fed for 28 days. Dogs were then abruptly switched to a canned diet and fed for 14 days, with fecal samples collected before and 2, 6, 10, and 14 days after diet change. All data were analyzed using the Mixed Models procedure of SAS 9.4, testing the effects of treatment, time, and treatment*time interactions. Treatment*time interactions were not observed, but the abrupt diet change reduced (p < 0.0001) fecal DM content, increased (p < 0.0001) fecal scores and pH, and reduced (p < 0.0001) fecal bacterial species richness and phylogenetic diversity. Diet change also increased (p < 0.001) fecal Bacteroidota, Fusobacteriota, and Proteobacteria, decreased (p < 0.001) fecal Firmicutes, and altered ~40 fecal bacterial genera relative abundances. Diet-induced changes were minimally impacted by B. coagulans, but fecal scores tended to be lower (i.e., firmer stools; p < 0.10), fecal E. coli and Faecalibacterium abundances were greater (p < 0.05), and fecal bacterial phylogenetic diversity was higher (p < 0.05) in dogs supplemented with the low dose than in controls. Our results demonstrate that abruptly transitioning dogs from a kibble to a canned diet negatively influences fecal characteristics and considerably shifts the composition of the fecal microbiota. Supplementation with B. coagulans did not mitigate the diet-induced shifts to fecal characteristics and most of the microbial taxa, although the low dose impacted some microbial taxa. Further investigation into optimal inclusion levels in pet foods is warranted.

Passive rewilding is increasingly seen as a promising tool to counterbalance biodiversity losses and recover native forest ecosystems. One key question, crucial to understanding assembly processes and conservation issues underlying land-use change, is the extent to which functional and phylogenetic diversity may recover in spontaneous recent woodlands. Here, we compared understorey plant communities of recent woodlands (which result from afforestation on agricultural lands during the 20th century) with those of ancient forests (uninterrupted for several centuries) in a hotspot of farmland abandonment in western Europe. We combined taxonomic, functional, and phylogenetic diversity metrics to detect potential differences in community composition, structure (richness, divergence), conservation importance (functional originality and specialization, evolutionary distinctiveness) and resilience (functional redundancy, response diversity). The recent and ancient forests harbored clearly distinct compositions, especially regarding the taxonomic and phylogenetic facets. Recent woodlands had higher taxonomic, functional and phylogenetic richness and a higher evolutionary distinctiveness, whereas functional divergence and phylogenetic divergence were higher in ancient forests. On another hand, we did not find any significant differences in functional specialization, originality, redundancy, or response diversity between recent and ancient forests. Our study constitutes one of the first empirical pieces of evidence that recent woodlands may spontaneously regain plant communities phylogenetically rich and functionally resilient, at least as much as those of ancient relict forests. As passive rewilding is the cheapest restoration method, we suggest that it should be a very useful tool to restore and conserve native forest biodiversity and functions, especially when forest areas are restricted and fragmented.

Disentangling the distribution patterns of biodiversity along altitudinal gradients and their drivers has been a hot topic in ecological research. Different forest strata show multiple distribution patterns influenced by different community assembly mechanisms. Here, we measure the dominant ecological processes affecting three forest strata (tree, shrub, and herb layers) along altitudinal gradients. We sampled plants with different forest strata in 21 plots located from 2500 to 3700 m in Lasha Mountain, northwestern Yunnan. The taxonomic alpha diversity of the herb layer showed a monotonic decreasing trend with increasing altitude, while the shrub layer was characterized by a single peak, and the tree layer showed no significant change with increasing altitude. We observed a decreasing pattern of phylogenetic diversity with increasing altitude in the herb layer, whereas phylogenetic diversity did not change in the tree and shrub layers. The phylogenetic structure of these three layers showed the same pattern: phylogenetic clustering at low altitudes and overdispersion at middle and high altitudes. The diversity and phylogenetic structure of the herb layer were driven by climate (average dry season precipitation) and topographic (slope and aspect) factors, while shrub layer diversity was mainly influenced by tree layer richness. Overall, the phylogenetic structure pattern of the three forest strata changed from clustered to overdispersed with increasing altitude, indicating that environmental filtering was the main driver at low altitudes, while interspecific competition dominated at middle and high altitudes.

The relative degree to which stochastic and deterministic processes underpin community assembly is a central problem in ecology. Quantifying local-scale phylogenetic and functional beta diversity may shed new light on this problem. We used species distribution, soil, trait and phylogenetic data to quantify whether environmental distance, geographic distance or their combination are the strongest predictors of phylogenetic and functional beta diversity on local scales in a 20-ha tropical seasonal rainforest dynamics plot in southwest China. The patterns of phylogenetic and functional beta diversity were generally consistent. The phylogenetic and functional dissimilarity between subplots (10 × 10 m, 20 × 20 m, 50 × 50 m and 100 × 100 m) was often higher than that expected by chance. The turnover of lineages and species function within habitats was generally slower than that across habitats. Partitioning the variation in phylogenetic and functional beta diversity showed that environmental distance was generally a better predictor of beta diversity than geographic distance thereby lending relatively more support for deterministic environmental filtering over stochastic processes. Overall, our results highlight that deterministic processes play a stronger role than stochastic processes in structuring community composition in this diverse assemblage of tropical trees.

Understanding how different land-use types shape soil bacterial communities and functions is critical for promoting sustainable land management and ecological restoration in fragile karst regions. This study evaluated the effects of different land-use types (pitaya [HF], maize [MF], sugarcane [SF], and paddy [PF] fields, forestland [FL], and grassland [AF]) on soil bacterial diversity, community composition, functional potentials, and co-occurrence networks in karst regions. The results showed that HF, MF, and PF exhibited the highest bacterial diversity (Shannon index), whereas SF had the lowest possibly because of continuous cropping and fertilization. Variance partitioning analysis revealed that soil bacterial community composition and functional potential were largely explained by the combined effects of land-use type and soil properties (34.8% for composition and 59.7% for functional potential), suggesting that land-use effects on bacterial communities are mainly mediated through changes in soil physicochemical properties. Hierarchical partitioning analysis further identified that soil texture, particularly silt and sand, and pH were the primary factors shaping bacterial community composition, whereas pH was the dominant driver of functional potential. Functional analysis indicated that HF enhanced nitrogen cycling processes, such as nitrification, aerobic nitrite oxidation, and aerobic ammonia oxidation; SF promoted carbon-related functions, including chemoheterotrophy, aerobic chemoheterotrophy, and cellulolysis; and PF favored iron and sulfur respiration. Co-occurrence network analysis demonstrated that HF had the most complex microbial interactions, likely attributable to no-tillage practices and favorable soil conditions, whereas PF showed the lowest network connectivity. Core bacterial groups such as Acidobacteria, Proteobacteria, Chloroflexi, and Actinobacteria, dominated in abundance but also functioned as keystone taxa, suggesting their critical roles in driving nutrient cycling and maintaining ecological stability. These findings suggest that no-till pitaya cultivation may help improve soil microbial diversity, functional potential, and ecological stability in fragile karst ecosystems, indicating its potential as a sustainable agricultural land-use practice. However, long-term monitoring and adaptive management are necessary to ensure sustained soil health.

Shifts in soil microbial communities over altitudinal gradients and the driving factors are poorly studied. Their elucidation is indispensable to gain a comprehensive understanding of the response of ecosystems to global climate change. Here, we investigated soil archaeal, bacterial, and fungal communities at four Alpine forest sites representing a climosequence, over an altitudinal gradient from 545 to 2000 m above sea level (asl), regarding abundance and diversity by using qPCR and Illumina sequencing, respectively. Archaeal community was dominated by Thaumarchaeota, and no significant shifts were detected in abundance or community composition with altitude. The relative bacterial abundance increased at higher altitudes, which was related to increasing levels of soil organic matter and nutrients with altitude. Shifts in bacterial richness and diversity as well as community structure (comprised basically of Proteobacteria, Acidobacteria, Actinobacteria, and Bacteroidetes) significantly correlated with several environmental and soil chemical factors, especially soil pH. The site at the lowest altitude harbored the highest bacterial richness and diversity, although richness/diversity community properties did not show a monotonic decrease along the gradient. The relative size of fungal community also increased with altitude and its composition comprised Ascomycota, Basidiomycota, and Zygomycota. Changes in fungal richness/diversity and community structure were mainly governed by pH and C/N, respectively. The variation of the predominant bacterial and fungal classes over the altitudinal gradient was the result of the environmental and soil chemical factors prevailing at each site.Electronic supplementary materialThe online version of this article (doi:10.1007/s00248-016-0748-2) contains supplementary material, which is available to authorized users.

Erosion and deposition divergently affect the structure of soil bacterial communities and functionality

Soil bacterial communities are a crucial biological indicator of soil health and crop performance; however, their response to climate change remains poorly understood. Wild blueberry farms are experiencing unprecedented temperature changes, which may exacerbate microbial responses and potentially harm the crop. Here, we aimed to elucidate the response of bacterial communities in wild blueberry fields to warming. We employed passive and active open-top chambers to simulate climate warming scenarios, which elevated atmospheric temperatures by 1.2 and 3.3°C, respectively. Soils in the active warming treatment exhibited significantly lower water content than in ambient conditions. Overall soil bacterial diversity and richness under the warming (passive and active) treatments and ambient controls did not demonstrate significant differences after 2 years of warming. However, we found significantly higher bacterial evenness and diversity under warming treatments in the early growing season (June). Our study found pronounced seasonal shifts in the evenness and diversity of bacteria in wild blueberry soils, suggesting that the variation in bacterial community structure may be more influenced by seasonal changes in temperature and plant activity than by warming treatments. Our study reveals the limited impact of warming on overall soil bacterial diversity in a temperate crop, but the seasonal dynamics of bacterial diversity and composition are sensitive to warming. The increased bacterial evenness and diversity under warming treatments in June could be attributed to advanced plant phenology, indicating a potential future shift in seasonal dynamics of bacterial activity under global warming.

One of soil microbiology's most intriguing puzzles is how so many different bacterial species can coexist in small volumes of soil when competition theory predicts that less competitive species should decline and eventually disappear. We provide evidence supporting the theory that low pore connectivity caused by low water potential (and therefore low water content) increases the diversity of a complex bacterial community in soil. We altered the pore connectivity of a soil by decreasing water potential and increasing the content of silt- and clay-sized particles. Two textures were created, without altering the chemical properties or mineral composition of the soil, by adding silt- and clay-sized particles of quartz to a quartz-based sandy soil at rates of 0% (sand) or 10% (silt+clay). Both textures were incubated at several water potentials, and the effect on the active bacterial communities was measured using terminal restriction fragment length polymorphism (TRFLP) of bacterial 16S rRNA. Bacterial richness and diversity increased as water potential decreased and soil became drier (P < 0.012), but they were not affected by texture (P > 0.553). Bacterial diversity increased at water potentials of <or=2.5 kPa in sand and <or=4.0 kPa in silt+clay, equivalent to <or=56% water-filled pore space (WFPS) in both textures. The bacterial community structure in soil was affected by both water potential and texture (P < 0.001) and was correlated with WFPS (sum of squared correlations [delta(2)] = 0.88, P < 0.001). These findings suggest that low pore connectivity is commonly experienced by soil bacteria under field conditions and that the theory of pore connectivity may provide a fundamental principle to explain the high diversity of bacteria in soil.

Soil bacterial communities of wheat vary across the growing season and among dryland farming systems