Fungal rather than bacterial communities are stabilized under soil salinization in the Taklamakan desert
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PROVIDER: PRJEB52403 | ENA |
REPOSITORIES: ENA
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Project description:Changes in bacterial communities stability to soil salinization
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Project description:Soil salinization Genome sequencing and assembly
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Project description:Salinization poses great threats to soil fungal communities that would cause the losses of ecosystems services. Soil fungal communities are composed of different functional guilds such as saprotrophic, symbiotrophic, and pathotrophic fungi, and each guild includes many rare taxa and a few abundant taxa. Despite of low abundance, rare taxa may be crucial in determining the responses of entire soil fungal communities to salinization. However, it remains poorly understood how rare taxa mediate the impacts of soil salinization on soil fungal community structure. Here, we took advantage of a salinity gradient in a desert ecosystem ranging from 0.60 to 31.09 g kg-1 that was created by a 12-year saline-water irrigation and assessed how the rare vs. abundant taxa of soil saprotrophic, symbiotrophic, and pathotrophic fungi respond to soil salinization through changes in the community biodiversity and composition. We found that the rare taxa of soil saprotrophic, symbiotrophic, and pathographic fungi were more sensitive to changes in soil salinity compared to the abundant taxa. In addition, the community composition of rare taxa of the saprotrophic and pathotrophic fungi not the symbiotrophic fungi was positively associated with soil salinity change. However, the symbiotrophic fungi showed greater variations in the species richness along the salinity gradient. These findings highlight the importance to differentiate rare taxa in predicting how the biodiversity and functional groups of soil fungal communities respond to soil salinization.
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Project description:Freshwater salinization is an escalating global environmental issue that threatens freshwater biodiversity, including fish populations. This study aims to uncover the molecular basis of salinity physiological responses in a non-native minnow species (Phoxinus septimaniae x P. dragarum) exposed to saline effluents from potash mines in the Llobregat River, Barcelona, Spain. Employing high-throughput mRNA sequencing and differential gene expression analyses, brain, gills, and liver tissues collected from fish at two stations (upstream and downstream of saline effluent discharge) were examined. Salinization markedly influenced global gene expression profiles, with the brain exhibiting the most differentially expressed genes, emphasizing its unique sensitivity to salinity fluctuations. Pathway analyses revealed the expected enrichment of ion transport and osmoregulation pathways across all tissues. Furthermore, tissue-specific pathways associated with stress, reproduction, growth, immune responses, methylation, and neurological development were identified in the context of salinization. Rigorous validation of RNA-seq data through quantitative PCR (qPCR) underscored the robustness and consistency of our findings across platforms. This investigation unveils intricate molecular mechanisms steering salinity physiological response in non-native minnows confronting diverse environmental stressors. This comprehensive analysis sheds light on the underlying genetic and physiological mechanisms governing fish physiological response in salinity-stressed environments, offering essential knowledge for the conservation and management of freshwater ecosystems facing salinization.
2024-07-02 | GSE271215 | GEO
Project description:The aim of this study was to determine whether the soil faunal-microbial interaction complexity (SFMIC) is a significant factor influencing the soil microbial communities and the willow growth in the context of PAH contamination. The SFMIC treatment had eight levels: just the microbial community, or the microbial community with nematodes, springtails, earthworms and all the possible combinations. SFMIC affected the height and biomass of willows after eight weeks or growth. SFMIC affected the structure and the composition of the bacterial, archaeal and fungal communities, with significant effects of SFMIC on the relative abundance of fungal genera such as Sphaerosporella, a known willow symbiont during phytoremediation, and bacterial phyla such as Actinobacteriota, containing many polycyclic aromatic hydrocarbons (PAH) degraders. These SFMIC effects on microbial communities were not clearly reflected in the community structure and abundance of PAH degraders, even though some degraders related to Actinobacteriota and the diversity of Gram-negative degraders were affected by the SFMIC treatments. Over 95% of PAH was degraded in all pots at the end of the experiment. Overall, our results suggest that, under our experimental conditions, SFMIC changes willow phytoremediation outcomes.
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Project description:Deserts cover a significant proportion of the Earth's surface and continue to expand as a consequence of climate change. Mutualistic arbuscular mycorrhizal (AM) fungi are functionally important plant root symbionts, and may be particularly important in drought stressed systems such as deserts. Here we provide a first molecular characterization of the AM fungi occurring in several desert ecosystems worldwide. We sequenced AM fungal DNA from soil samples collected from deserts in six different regions of the globe using the primer pair WANDA-AML2 with Illumina MiSeq. We recorded altogether 50 AM fungal phylotypes. Glomeraceae was the most common family, while Claroideoglomeraceae, Diversisporaceae and Acaulosporaceae were represented with lower frequency and abundance. The most diverse site, with 35 virtual taxa (VT), was in the Israeli Negev desert. Sites representing harsh conditions yielded relatively few reads and low richness estimates, for example, a Saudi Arabian desert site where only three Diversispora VT were recorded. The AM fungal taxa recorded in the desert soils are mostly geographically and ecologically widespread. However, in four sites out of six, communities comprised more desert-affiliated taxa (according to the MaarjAM database) than expected at random. AM fungal VT present in samples were phylogenetically clustered compared with the global taxon pool, suggesting that nonrandom assembly processes, notably habitat filtering, may have shaped desert fungal assemblages.
| S-EPMC7912695 | biostudies-literature
Project description:The response of microbial communities to continual and prolonged water exposure provides useful insight when facing global climate changes that cause increased and uneven precipitation and extreme rainfall events. In this study, we investigated an in situ manipulative experiment with four levels of water exposure (ambient precipitation +0%, +25%, +50%, and +100% of local annual mean precipitation) in a desert ecosystem of China. After 9 years of water addition, Illumina sequencing was used to analyze taxonomic compositions of the soil bacterial, archaeal, and fungal communities. The results showed significant increases in microbial biomass carbon (MBC) at higher amended precipitation levels, with the highest values reported at 100% precipitation. Furthermore, an increase in the bacterial species richness was observed along the water addition gradient. In addition, the relative abundance of several bacterial phyla, such as Proteobacteria, significantly increased, whereas that of some drought-tolerant taxa, including Actinobacteria, Firmicutes, and Bacteroidetes, decreased. In addition, the phyla Planctomycetes and Nitrospirae, associated with nitrification, positively responded to increased precipitation. Archaeal diversity significantly reduced under 100% treatment, with changes in the relative abundance of Thaumarchaeota and Euryarchaeota being the main contributors to shifts in the archaeal community. The fungal community composition was stable in response to water addition. Results from the Mantel test and structural equation models suggested that bacterial and archaeal communities reacted contrastingly to water addition. Bacterial community composition was directly affected by changing soil moisture and temperature, while archaeal community composition was indirectly affected by changing nitrogen availability. These findings highlight the importance of soil moisture and nitrogen in driving microbial responses to long-term precipitation changes in the desert ecosystem.
| S-EPMC8147197 | biostudies-literature
Project description:Nitrogen (N) deposition is a worldwide issue caused by human activity. Long-term deposition of N strongly influences plant productivity and community composition. However, it is still unclear how the microbial community responds to long-term N addition in a desert ecosystem. Therefore, a long-term experiment was conducted in the Gurbantonggut Desert in northwestern China in 2015. Four N addition rates, 0 (CK), 5 (N1), 20 (N2), and 80 (N3) kg N ha-1 yr.-1, were tested and the soil was sampled after 6 years of N addition. High-throughput sequencing (HTS) was used to analyze the soil microbial composition. The HTS results showed that N addition had no significant effect on the bacterial α-diversity and β-diversity (p > 0.05) but significantly reduced the archaeal β-diversity (p < 0.05). The fungal Chao1 and ACE indexes in the N2 treatment increased by 24.10 and 26.07%, respectively. In addition, N addition affected the bacterial and fungal community structures. For example, compared to CK, the relative abundance of Actinobacteria increased by 17.80%, and the relative abundance of Bacteroidetes was reduced by 44.46% under N3 treatment. Additionally, N addition also changed the bacterial and fungal community functions. The N3 treatment showed increased relative abundance of nitrate-reducing bacteria (27.06% higher than CK). The relative abundance of symbiotrophic fungi was increased in the N1 treatment (253.11% higher than CK). SOC and NH4 +-N could explain 62% of the changes in the fungal community function. N addition can directly affect the bacterial community function or indirectly through NO3 --N. These results suggest that different microbial groups may have various responses to N addition. Compared with bacteria and fungi, the effect of N addition was less on the archaeal community. Meanwhile, N-mediated changes of the soil properties play an essential role in changes in the microbial community. The results in the present study provided a reliable basis for an understanding of how the microbial community in a desert ecosystem adapts to long-term N deposition.
| S-EPMC9606763 | biostudies-literature
Project description:Desert shrub rhizosphere bacterial communities Raw sequence reads
| PRJNA738934 | ENA
Project description:The effects of increased nitrogen (N) deposition on desert ecosystems have been extensively studied from a plant community perspective. However, the response of soil microbial communities, which play a crucial role in nutrient cycling, to N inputs and plant community types remains poorly understood. In this study, we conducted a two-year N-addition experiment with five gradients (0, 10, 30, 60, and 120 kg N ha-1 year-1) to evaluate the effect of increased N deposition on soil bacterial and fungal communities in three plant community types, namely, Alhagi sparsifolia Shap., Karelinia caspia (Pall.) Less. monocultures and their mixed community in a desert steppe located on the southern edge of the Taklimakan Desert, Northwest China. Our results indicate that N deposition and plant community types exerted an independent and significant influence on the soil microbial community. Bacterial α-diversity and community dissimilarity showed a unimodal pattern with peaks at 30 and 60 kg N ha-1 year-1, respectively. By contrast, fungal α-diversity and community dissimilarity did not vary significantly with increased N inputs. Furthermore, plant community type significantly altered microbial community dissimilarity. The Mantel test and redundancy analysis indicated that soil pH and total and inorganic N (NH4+ and NO3-) levels were the most critical factors regulating soil microbial communities. Similar to the patterns observed in taxonomic composition, fungi exhibit stronger resistance to N addition compared to bacteria in terms of their functionality. Overall, our findings suggest that the response of soil microbial communities to N deposition is domain-specific and independent of desert plant community diversity, and the bacterial community has a critical threshold under N enrichment in arid deserts.
| S-EPMC10609353 | biostudies-literature