FIGURE 1 - available via license: Creative Commons Attribution 4.0 International
Content may be subject to copyright.
| Map showing the location of Mount Wutai and the sampling sites. High elevational gradient (HEG) (2900-3055 m) including five different elevation sampling sites (HEG1, HEG2, HEG3, HEG4, and HEG5), both medium elevational gradient (MEG) (2500-2800 m) (MEG1, MEG2, MEG3, and MEG4) and low elevational gradients (LEG) (2000-2300 m) (LEG1, LEG2, LEG3, and LEG4) including four different elevation sampling sites.
Source publication
A core issue in microbial ecology is the need to elucidate the ecological processes and underlying mechanisms involved in microbial community assembly. However, the extent to which these mechanisms differ in importance based on traits of taxa with different niche breadth is poorly understood. Here, we used high-throughput sequencing to examine the...
Contexts in source publication
Context 1
... this study was conducted to : (1) describe the diversity, structure and biogeographical patterns of soil bacterial communities and subcommunities (specialists, generalists and other taxa) across elevational gradients along the slope of Mount Wutai; (2) explore the variations and drivers related to the community assembly of soil bacterial subcommunities among elevational gradients; (3) quantify the relative roles of environmental selection and space distance in the community assembly of soil bacterial taxa and differentiate the community assembly mechanisms of bacterial subcommunities with different niche breadth across elevational gradients. (Figure 1). The climate is warm temperate semi-humid. ...
Context 2
... with a B-value >8.7 were considered as habitat generalists that were present and more evenly distributed along a wider range of habitats, while OTUs with a B-value <1.5 were defined as habitat specialists ( Logares et al., 2013). B-values >8.7 and B-value <1.5 were chosen because both values were within the outlier area of the B distribution ( Figure S1). ...
Similar publications
Two contradictory niche-based processes, environmental filtering and competitive exclusion, are important ecological processes in community assembly. Quercus wutaishanica forests are the climax communities in the Qinling Mountains and the Loess Plateau, China. Since these areas are characterized by different climate and evolutionary histories, thes...
Citations
... A stochastic process refers to unpredictable events in an ecosystem governed by random factors, whereas a deterministic process is characterized by predictable and systematic influences from ecological factors. Most studies have shown that bacterial communities are influenced by deterministic (niche theory) and stochastic processes (neutral theory) [14]. In addition, studies have shown that environmental factors can regulate the balance between deterministic and stochastic processes [15]. ...
... Significant differences are found in the physicochemical properties of woody plants and soil under different altitude gradients [31,54]. The lower diversity of specialized bacterial species at high altitudes may be due to harsh environmental conditions (including higher solar radiation, large daily temperature fluctuations, high wind exposure, etc.) [14]. The results of this study showed that the diversity of specialized bacterial species was not signif-icantly varied under different altitude gradients probably because specialized species had higher fitness under certain environmental conditions, whereas generalized species had consistent fitness across gradients of different conditions [55][56][57]. ...
Soil bacteria are an important part of the forest ecosystem, and they play a crucial role in driving energy flow and material circulation. Currently, many uncertainties remain about how the composition and distribution patterns of bacterial communities change along altitude gradients, especially in forest ecosystems with strong altitude gradients in climate, vegetation, and soil properties. Based on dynamic site monitoring of the Baiyun Mountain Forest National Park (33°38′–33°42′ N, 111°47′–111°51′ E), this study used Illumina technology to sequence 120 soil samples at the site and explored the spatial distribution mechanisms and ecological processes of soil bacteria under different altitude gradients. Our results showed that the composition of soil bacterial communities varied significantly between different altitude gradients, affecting soil bacterial community building by influencing the balance between deterministic and stochastic processes; in addition, bacterial communities exhibited broader ecological niche widths and a greater degree of stochasticity under low-altitude conditions, implying that, at lower altitudes, community assembly is predominantly influenced by stochastic processes. Light was the dominant environmental factor that influenced variation in the entire bacterial community as well as other taxa across different altitude gradients. Moreover, changes in the altitude gradient could cause significant differences in the diversity and community composition of bacterial taxa. Our study revealed significant differences in bacterial community composition in the soil under different altitude gradients. The bacterial communities at low elevation gradients were mainly controlled by stochasticity processes, and bacterial community assembly was strongly influenced by deterministic processes at middle altitudes. Furthermore, light was an important environmental factor that affects differences. This study revealed that the change of altitude gradient had an important effect on the development of the soil bacterial community and provided a theoretical basis for the sustainable development and management of soil bacteria.
... Therefore, the elevational patterns of biodiversity and adaptability could reflect the responses of ecosystem to future climatic scenarios (Frac et al., 2018). Yet, despite many practical studies have revealed elevational patterns of the diversity in vertebrates, macroinvertebrates, and plants (Currie & Paquin, 1987;McCain, 2005;Renaud et al., 2009), elevational patterns of soil microorganisms have limited empirical investigation, and they are inconsistent in previous studies, such as no obvious pattern (Fierer et al., 2011;Shen et al., 2013), a decline (Bahram et al., 2012;Bryant et al., 2008;Ji et al., 2022;Luo et al., 2019), hump-shaped (Miyamoto et al., 2014;Ren et al., 2021;Zhang et al., 2014), and U-shaped (Li et al., 2016). Those inconsistencies maybe related to the differences in trophic levels (fungi, bacteria, etc.), taxonomic groups (phylum level), and climatic zones (Wang et al., 2017). ...
... Based on these findings, we emphasize the importance of considering regional climatic conditions and taxonomic resolutions when studying elevation patterns of microbial diversity. and no obvious change showed in the cold-temperate forest (Ji et al., 2022;Luo et al., 2019;Nottingham et al., 2018;Ren et al., 2021;Shen et al., 2013). The different elevation patterns in bacterial species richness suggest that different environmental factors (climatic factors, spatial factors, historical factors, and disturbance factors) may be at play in each climatic region (Chalmandrier et al., 2019;Zhu et al., 2020). ...
... Bacterial richness and evenness increase with increasing pH and reach a maximum at neutral pH ( Figure 8), which is consistent with the findings of previous studies (Fierer & Jackson, 2006;Shen et al., 2019). Deviation from the neutral pH value may exert physiological constraints and the energy costs on microorganisms, which may limit the possibility of multiple species living in the same niche (Luo et al., 2019;Tripathi et al., 2012). Bacterial richness and evenness are mainly controlled by soil pH, which is consistent with the results of other microbial diversity studies (Luo et al., 2019;Shen et al., 2019;Wang et al., 2017), but the control factors for fungal richness and evenness are different. ...
Understanding the elevational patterns of soil microbial diversity is crucial for microbial biogeography, yet the elevational patterns of diversity across different climatic zones, trophic levels, and taxonomic levels remain unclear. In this study, we investigated the elevational patterns of species richness, species evenness and the relationship between species richness and evenness (RRE) in the forest soil bacterial and fungal communities and individual phyla across three climatic zones (tropical, subtropical, and cold temperate). Our results revealed that soil bacterial richness (alpha diversity) decreased with elevation, while fungal richness exhibited a hump‐shaped pattern in the tropical and cold‐temperate forests. Elevational patterns of evenness in bacterial and fungal communities showed the hump‐shaped pattern across climatic zones, except for bacterial evenness in the tropical forest. Both bacterial and fungal richness and evenness were positively correlated in the subtropical and cold‐temperate forests, while negatively correlated for bacteria in the tropical forest. The richness and evenness of soil microorganisms across different regions were controlled by climatic and edaphic factors. Soil pH was the most important factor associated with the variations in bacterial richness and evenness, while mean annual temperature explained the major variations in fungal richness. Our results addressed that the varieties of elevational patterns of microbial diversity in climatic zones and taxonomic levels, further indicating that richness and evenness may respond differently to environmental gradients.
... In this study, we aimed to (i) investigate distribution patterns, evolutionary characteristics, environmental adaptability, and ecological community assembly processes of bacterioplankton generalists and specialists before and after dredging, and (ii) estimate community difference between generalists and specialists before dredging and afterwards. Considering generalists prevail in habitat niche (Luo et al., 2019;Xu et al., 2021), we hypothesized that bacterioplankton generalists rather than specialists would display stronger environmental adaptability and tend to be affected more by stochasticity. Given microbial communities show resistance to environmental change and resilience to original state (Griffiths and Philippot, 2013;Zhang et al., 2017), we also hypothesized that a short-term dredging implementing from August 2017 to March 2018 might not result in reversible community difference between bacterioplankton generalists and specialists. ...
... The generalists occupied higher habitat niche than specialists, but the specialists displayed higher abundance and richness. The results are similar to prior findings (Luo et al., 2019;Mo et al., 2021), and this might be the intrinsic properties of generalists and specialists. Generalists rather than specialists contributed more to Proteobacteria, which is in sympathy with prior findings (Liao et al., 2016;Luo et al., 2019). ...
... The results are similar to prior findings (Luo et al., 2019;Mo et al., 2021), and this might be the intrinsic properties of generalists and specialists. Generalists rather than specialists contributed more to Proteobacteria, which is in sympathy with prior findings (Liao et al., 2016;Luo et al., 2019). Specialists rather than generalists contributed more to Actinobacteria, which differs from prior findings (Liao et al., 2016;Luo et al., 2019). ...
Understanding response of bacterioplankton community responsible for maintaining ecological functions of aquatic ecosystems to environmental disturbance is an important subject. However, it remains largely unclear how bacterioplankton generalists and specialists respond to dredging disturbance. Illumina MiSeq sequencing and statistical analyses were used to evaluate landscape patterns, evolutionary potentials, environmental adaptability, and community assembly processes of generalists and specialists in response to dredging in eutrophic Lake Nanhu. The Proteobacteria and Actinobacteria dominated bacterioplankton communities of generalists and specialists, and abundances of Proteobacteria decreased and Actinobacteria increased after dredging. The generalists displayed higher phylogenetic distance, richness difference, speciation rate, extinction rate, and diversification rate as well as stronger environmental adaptation than that of specialists. In contrast, the specialists rather than generalists showed higher community diversity, taxonomic distance, and species replacement as well as closer phylogenetic clustering. Stochastic processes dominated community assemblies of generalists and specialists, and stochasticity exhibited a larger effect on community assembly of generalists rather than specialists. Our results emphasized that lake dredging could change landscape patterns of bacterioplankton generalists and specialists, whereas the short-term dredging conducted within one year was unable to reverse community difference between generalists and specialists. Our findings extend our understanding of how bacterioplankton generalists and specialists responding to dredging disturbance, and these findings might in turn call on long-term dredging for better ecological restoration of eutrophic lakes.
... Two broad paradigms have been suggested to answer this question. The first is that niche generalism and specialism are governed by trade-offs between performance efficiency and breadth (4)(5)(6)(7)(8)(9). For example, replicate populations of Escherichia coli grown in medium containing only glucose repeatedly evolved increased ability to use glucose but showed a reduction in their ability to catabolize other carbon sources (10). ...
Organisms exhibit extensive variation in ecological niche breadth, from very narrow (specialists) to very broad (generalists). Paradigms proposed to explain this variation either invoke trade-offs between performance efficiency and breadth or underlying intrinsic or extrinsic factors. We assembled genomic (1,154 yeast strains from 1,049 species), metabolic (quantitative measures of growth of 843 species in 24 conditions), and ecological (environmental ontology of 1,088 species) data from nearly all known species of the ancient fungal subphylum Saccharomycotina to examine niche breadth evolution. We found large interspecific differences in carbon breadth stem from intrinsic differences in genes encoding specific metabolic pathways but no evidence of trade-offs and a limited role of extrinsic ecological factors. These comprehensive data argue that intrinsic factors driving microbial niche breadth variation.
One-Sentence Summary
A nearly complete genomic catalog of the yeast subphylum illuminates the evolution of their diverse ecologies and metabolisms.
... Nutrients are essential elements for microbial growth, and the abundance of planktonic bacteria in the eutrophic reservoir is thus higher than that in the oligotrophic reservoir (Yue et al. 2021). Water temperature is usually associated with geographical variables such as altitude and solar radiation and can affect the growth and reproduction of microorganisms (Shapiro et al. 2012;Luo et al. 2019). It has been found that water temperature, but not other factors, significantly influences the structure of the planktonic bacterial community in some reservoirs (Chen et al. 2021;Li et al. 2022). ...
Background
Planktonic bacteria and archaea play a key role in river nutrient biogeochemical cycling; however, their respective community assembly and how to maintain their diversity are not well known in dammed rivers. Therefore, a seasonal survey of planktonic bacterial and archaeal community compositions and related environmental factors was conducted in 16 cascade reservoirs and corresponding river waters on the Wujiang River and the Pearl River in southwest China to understand the above mechanisms.
Results
Deterministic processes dominated bacterial and archaeal community assembly. The structural equation models showed that water temperature can directly or indirectly affect the microbial diversity. Interestingly, planktonic bacterial diversity increased with increasing water temperature, while archaea showed the opposite trend; the overall diversity of bacteria and archaea was no significant changes with changeable water temperature. Abundant microbes had a stronger distance–decay relationship than middle and rare ones, and the relationship was stronger in winter and spring than in summer and autumn.
Conclusions
Planktonic bacteria and archaea in dammed rivers had different biogeographic distributions, and water temperature was a key controlling factor. The different responses of planktonic bacterial and archaeal diversity to water temperature could be due to their different phylogenetic diversity. This ultimately maintained the stability of total microbial community diversity. This study reveals the different responses of planktonic bacteria and archaea to water temperature and perfects the theoretical framework for planktonic microbial biogeography in dammed rivers.
... Generalists are metabolically more flexible than specialists, resulting in selective advantage in frequently disturbed ecosystems ; these might thus be favored in the atmosphere. The relative abundance of Proteobacteria and Actinobacteria, which include higher proportions of generalists than other phyla, increases with altitude in soils (Luo et al., 2019); these are also frequent in viable airborne assemblages (Vaïtilingom et al., 2012). ...
The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.
... 25 samples (approximately 10% of the total samples) were selected for network analysis and SEM. In this study, a B-value of > 78 was chosen as a cutoff criterion for generalists, as this value lies within the outlier area of the B-value distribution [44,45], whereas ASVs with B-values of < 22 were regarded as specialists (lower quartile) (Fig. S1), and the remaining ASVs were regarded as common taxa. The Shannon diversity index was calculated using functions in Vegan. ...
... These two groups, apart from being keystone microbes, were found to be the most dominant groups in both generalists (Rhizobiales) and specialists (Ktedonobacterales), highlighting their essential roles in the study sites. Previous studies have reported that Rhizobiales and Acidobacteriales are dominant bacterial groups in the Arctic region [45,46]. The average relative abundance of Rhizobiales in our study was 12.2% ± 2.3%, which is approximately five-fold higher than that in unplanted soil environments and similar to that in plant microbiota (5-17%) [25]. ...
Understanding the variability of microbial niches and their interaction with abiotic and biotic factors in the Arctic can provide valuable insights into microbial adaptations to extreme environments. This study investigates the structure and diversity of soil bacterial communities obtained from sites with varying vegetation coverage and soil biogeochemical properties in the low Arctic tundra and explores how bacteria interact under different environmental parameters. Our findings reveal differences in bacterial composition and abundance among three bacterial niche breadths (specialists, common taxa, and generalists). Co-occurrence network analysis revealed Rhizobiales and Ktedonobacterales as keystone taxa that connect and support other microbes in the habitat. Low-elevation indicators, such as vascular plants and moisture content, were correlated with two out of three generalist modular hubs and were linked to a large proportion of generalists’ distribution (18%). Structural equation modeling revealed that generalists’ distribution, which influenced the remaining microbial communities, was mainly regulated by vegetation coverage as well as other abiotic and biotic factors. These results suggest that elevation-dependent environmental factors directly influence microbial community structure and module formation through the regulation of generalists’ distribution. Furthermore, the distribution of generalists was mainly affected by macroenvironment filtering, whereas the distribution of specialists was mainly affected by microenvironment filtering (species-engineered microbial niche construction). In summary, our findings highlight the strong top–down control exerted by vegetation on generalists’ distribution, which in turn shapes the overall microbial community structure in the low Arctic tundra.
... Generalists are more adept at adapting to adverse conditions, while specialists are less tolerant to environmental disturbances (Sriswasdi et al., 2017). Studies have revealed that specialists are more heavily impacted by deterministic processes and are more susceptible to environmental filtering (Luo et al., 2019), while generalists are more prone to be governed by stochastic processes (Liao et al., 2016) due to their higher genetic potential for developing resistance mechanisms, such as dormancy . ...
... On the other hand, the proportion of generalists was found to be fewer, fitting to the lognormal distribution, and is expected to be driven by a niche-based model. Indeed, our Z-score variations showed that deterministic processes have a major influence on the assembly of generalists (Luo et al., 2019). ...
The conversion of natural grasslands to cultivated pastures has a profound effect on the soil habitat conditions, influencing the proportion of soil specialist and generalist microbes, with consequences for the assembly of microbial communities. This often leads to the homogenization of the microbial community and thus favoring stochastic assembly processes. However, there is still a gap in understanding the effect of conversion from natural grasslands to cultivated pastures on soil microbial ecological processes. Therefore, we aimed to investigate the assembly patterns of microbial communities and evaluate the ecological models for generalists and specialist microbes along a grassland management intensification gradient. Through 16S rRNA amplicon sequencing, we found that the conversion of natural grasslands to cultivated pastures has increased the number of microbial specialists, resulting in stochastic assembly processes due to the decrease in plant diversity. Moreover, the ecological processes governing the assembly of microbial communities were affected by soil and vegetation management. The perennial pasture was more affected by homogenizing selection, owing to the lower plant diversity and uniform plant covering and root development. We have found that the generalists in the grasslands are shaped by niche-based models, while the specialists in natural grasslands are more stochastic in nature. For improved pastures, we have found that lognormal and preemption models are more predominant, suggesting that homogenizing dispersal is more predominant than variable selection. We highlight it is essential to comprehend these assembly models and ecological processes to ensure plant-microbe supporting and provisioning ecosystem services for cattle, and humans while establishing management strategies and conservation policy priorities.
... Based on this definition, Sriswasdi et al. 27 suggested an important evolutionary role for generalist species in maintaining taxonomic diversity, with generalists having higher speciation rates and persistence advantages over specialists. Others defined the niche breadth of an organism by the uniformity of its distribution across habitats 28 , suggesting that community assembly of specialists is driven by deterministic processes, whereas for generalists neutral processes are more important 29,30 . Notwithstanding these intriguing results, niche breadth studies based on occurrence in microbiomes have been sensitive to biases due to habitat definition and sample selection. ...
Generalists can survive in many environments, whereas specialists are restricted to a single environment. Although a classical concept in ecology, niche breadth has remained challenging to quantify for microorganisms because it depends on an objective definition of the environment. Here, by defining the environment of a microorganism as the community it resides in, we integrated information from over 22,000 environmental sequencing samples to derive a quantitative measure of the niche, which we call social niche breadth. At the level of genera, we explored niche range strategies throughout the prokaryotic tree of life. We found that social generalists include opportunists that stochastically dominate local communities, whereas social specialists are stable but low in abundance. Social generalists have a more diverse and open pan-genome than social specialists, but we found no global correlation between social niche breadth and genome size. Instead, we observed two distinct evolutionary strategies, whereby specialists have relatively small genomes in habitats with low local diversity, but relatively large genomes in habitats with high local diversity. Together, our analysis shines data-driven light on microbial niche range strategies.
... Acid mine drainage sludge also reduced the abundance and diversity of bacterial community in compost (Chi et al., 2022). pH was the main factor affecting the variation of generalists and specialists in compost (Luo et al., 2019). In addition, niche breadth and bacterial survival may be negatively correlated (Xing et al., 2019). ...
Aerobic composting renders the sauerkraut fermentation waste water harmless while adding soluble nutrients. Unravelling the bacterial community assembly processes, changes in community robustness and community cohesion and the relationship between them under composting treatment of sauerkraut fermentation waste water is an interesting topic. Sauerkraut fermentation waste water was used for composting, which increased bacterial linkages, community robustness, competitive behaviour during warming periods and cooperative behaviour during cooling periods, and the control of community assembly processes shifts from deterministic processes (variable selection) to stochastic processes (decentralised limitation). At the same time, the influence of community robustness and community cohesion on community assembly processes was increased. Community cohesion and robustness were significantly correlated with community function. These results indicate that community robustness and community cohesion are critical for the biological handling of hazardous substances.
