scholarly journals Microbial Diversity in Engineered Haloalkaline Environments Shaped by Shared Geochemical Drivers Observed in Natural Analogues

2015 ◽  
Vol 81 (15) ◽  
pp. 5026-5036 ◽  
Author(s):  
Talitha C. Santini ◽  
Lesley A. Warren ◽  
Kathryn E. Kendra
Keyword(s):  
Community Structure ◽  
Microbial Diversity ◽  
Fungal Community ◽  
Soda Lakes ◽  
Bauxite Residue ◽  
Environmental Parameters ◽  
Total Alkalinity ◽  
Content Type ◽  
Natural Analogues ◽  
Bauxite Residues

ABSTRACTMicrobial communities in engineered terrestrial haloalkaline environments have been poorly characterized relative to their natural counterparts and are geologically recent in formation, offering opportunities to explore microbial diversity and assembly in dynamic, geochemically comparable contexts. In this study, the microbial community structure and geochemical characteristics of three geographically dispersed bauxite residue environments along a remediation gradient were assessed and subsequently compared with other engineered and natural haloalkaline systems. In bauxite residues, bacterial communities were similar at the phylum level (dominated byProteobacteriaandFirmicutes) to those found in soda lakes, oil sands tailings, and nuclear wastes; however, they differed at lower taxonomic levels, with only 23% of operational taxonomic units (OTUs) shared with other haloalkaline environments. Although being less diverse than natural analogues, bauxite residue harbored substantial novel bacterial taxa, with 90% of OTUs nonmatchable to cultured representative sequences. Fungal communities were dominated byAscomycotaandBasidiomycota, consistent with previous studies of hypersaline environments, and also harbored substantial novel (73% of OTUs) taxa. In bauxite residues, community structure was clearly linked to geochemical and physical environmental parameters, with 84% of variation in bacterial and 73% of variation in fungal community structures explained by environmental parameters. The major driver of bacterial community structure (salinity) was consistent across natural and engineered environments; however, drivers differed for fungal community structure between natural (pH) and engineered (total alkalinity) environments. This study demonstrates that both engineered and natural terrestrial haloalkaline environments host substantial repositories of microbial diversity, which are strongly shaped by geochemical drivers.

scholarly journals Dominant Tree Species and Soil Type Affect the Fungal Community Structure in a Boreal Peatland Forest

2016 ◽  
Vol 82 (9) ◽  
pp. 2632-2643 ◽  
Author(s):  
Hui Sun ◽  
Eeva Terhonen ◽  
Andriy Kovalchuk ◽  
Hanna Tuovila ◽  
Hongxin Chen ◽  
...  
Keyword(s):  
Community Structure ◽  
Community Composition ◽  
High Throughput ◽  
Fungal Community ◽  
Tree Species ◽  
High Throughput Sequencing ◽  
Soil Layer ◽  
Fungal Community Composition ◽  
Content Type ◽  
Boreal Peatlands

ABSTRACTBoreal peatlands play a crucial role in global carbon cycling, acting as an important carbon reservoir. However, little information is available on how peatland microbial communities are influenced by natural variability or human-induced disturbances. In this study, we have investigated the fungal diversity and community structure of both the organic soil layer and buried wood in boreal forest soils using high-throughput sequencing of the internal transcribed spacer (ITS) region. We have also compared the fungal communities during the primary colonization of wood with those of the surrounding soils. A permutational multivariate analysis of variance (PERMANOVA) confirmed that the community composition significantly differed between soil types (P< 0.001) and tree species (P< 0.001). The distance-based linear models analysis showed that environmental variables were significantly correlated with community structure (P< 0.04). The availability of soil nutrients (Ca [P= 0.002], Fe [P= 0.003], and P [P= 0.003]) within the site was an important factor in the fungal community composition. The species richness in wood was significantly lower than in the corresponding soil (P< 0.004). The results of the molecular identification were supplemented by fruiting body surveys. Seven of the genera ofAgaricomycotinaidentified in our surveys were among the top 20 genera observed in pyrosequencing data. Our study is the first, to our knowledge, fungal high-throughput next-generation sequencing study performed on peatlands; it further provides a baseline for the investigation of the dynamics of the fungal community in the boreal peatlands.

scholarly journals Nutrient availability is a dominant predictor of soil bacterial and fungal community composition after nitrogen addition in subtropical acidic forests

PLoS ONE ◽  
2021 ◽  
Vol 16 (2) ◽  
pp. e0246263
Author(s):  
Juyan Cui ◽  
Xiaochun Yuan ◽  
Qiufang Zhang ◽  
Jiacong Zhou ◽  
Kaimiao Lin ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Fungal Community ◽  
Soil Microbial Community ◽  
N Addition ◽  
Subtropical Forests ◽  
Soil Microbial ◽  
Experimental Plots

Nutrient addition to forest ecosystems significantly influences belowground microbial diversity, community structure, and ecosystem functioning. Nitrogen (N) addition in forests is common in China, especially in the southeast region. However, the influence of N addition on belowground soil microbial community diversity in subtropical forests remains unclear. In May 2018, we randomly selected 12 experimental plots in a Pinus taiwanensis forest within the Daiyun Mountain Nature Reserve, Fujian Province, China, and subjected them to N addition treatments for one year. We investigated the responses of the soil microbial communities and identified the major elements that influenced microbial community composition in the experimental plots. The present study included three N treatments, i.e., the control (CT), low N addition (LN, 40 kg N ha-1 yr-1), and high N addition (HN, 80 kg N ha-1 yr-1), and two depths, 0−10 cm (topsoil) and 10−20 cm (subsoil), which were all sampled in the growing season (May) of 2019. Soil microbial diversity and community composition in the topsoil and subsoil were investigated using high-throughput sequencing of bacterial 16S rDNA genes and fungal internal transcribed spacer sequences. According to our results, 1) soil dissolved organic carbon (DOC) significantly decreased after HN addition, and available nitrogen (AN) significantly declined after LN addition, 2) bacterial α-diversity in the subsoil significantly decreased with HN addition, which was affected significantly by the interaction between N addition and soil layer, and 3) soil DOC, rather than pH, was the dominant environmental factor influencing soil bacterial community composition, while AN and MBN were the best predictors of soil fungal community structure dynamics. Moreover, N addition influence both diversity and community composition of soil bacteria more than those of fungi in the subtropical forests. The results of the present study provide further evidence to support shifts in soil microbial community structure in acidic subtropical forests in response to increasing N deposition.

scholarly journals Microbial Diversity in Deep-Subsurface Hot Brines of Northwest Poland: from Community Structure to Isolate Characteristics

2020 ◽  
Vol 86 (10) ◽  
Author(s):  
Agnieszka Kalwasińska ◽  
Arkadiusz Krawiec ◽  
Edyta Deja-Sikora ◽  
Marcin Gołębiewski ◽  
Przemysław Kosobucki ◽  
...  
Keyword(s):  
Community Structure ◽  
16S Rrna ◽  
Microbial Diversity ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Deep Subsurface ◽  
Content Type ◽  
Microbial Life ◽  
Bacillus Paralicheniformis ◽  
Low Diversity

ABSTRACT Deep-subsurface hot brines in northwest Poland, extracted through boreholes reaching 1.6 and 2.6 km below the ground surface, were microbiologically investigated using culture-independent and culture-dependent methods. The high-throughput sequencing of 16S rRNA gene amplicons showed a very low diversity of bacterial communities, which were dominated by phyla Proteobacteria and Firmicutes. Bacterial genera potentially involved in sulfur oxidation and nitrate reduction (Halothiobacillus and Methylobacterium) prevailed in both waters over the sulfate reducers (“Candidatus Desulforudis” and Desulfotomaculum). Only one archaeal taxon, affiliated with the order Thermoplasmatales, was detected in analyzed samples. Bacterial isolates obtained from these deep hot brines were closely related to Bacillus paralicheniformis based on the 16S rRNA sequence similarity. However, genomic and physiological analyses made for one of the isolates, Bacillus paralicheniformis strain TS6, revealed the existence of more diverse metabolic pathways than those of its moderate-temperature counterpart. These specific traits may be associated with the ecological adaptations to the extreme habitat, which suggest that some lineages of B. paralicheniformis are halothermophilic. IMPORTANCE Deep-subsurface aquifers, buried thousands of meters down the Earth’s crust, belong to the most underexplored microbial habitats. Although a few studies revealed the existence of microbial life at the depths, the knowledge about the microbial life in the deep hydrosphere is still scarce due to the limited access to such environments. Studying the subsurface microbiome provides unique information on microbial diversity, community structure, and geomicrobiological processes occurring under extreme conditions of the deep subsurface. Our study shows that low-diversity microbial assemblages in subsurface hot brines were dominated by the bacteria involved in biogeochemical cycles of sulfur and nitrogen. Based on genomic and physiological analyses, we found that the Bacillus paralicheniformis isolate obtained from the brine under study differed from the mesophilic species in the presence of specific adaptations to harsh environmental conditions. We indicate that some lineages of B. paralicheniformis are halothermophilic, which was not previously reported.

Changes of soil bacterial and fungal community structure along a natural aridity gradient in desert grassland ecosystems, Inner Mongolia

CATENA ◽  
2021 ◽  
Vol 205 ◽  
pp. 105470
Author(s):  
Shaokun Wang ◽  
Xiaoan Zuo ◽  
Tala Awada ◽  
Eduardo Medima-Roldán ◽  
Keting Feng ◽  
...  
Keyword(s):  
Community Structure ◽  
Fungal Community ◽  
Inner Mongolia ◽  
Desert Grassland ◽  
Aridity Gradient ◽  
Fungal Community Structure ◽  
Grassland Ecosystems ◽  
Soil Bacterial

scholarly journals Micro-Landscape Dependent Changes in Arbuscular Mycorrhizal Fungal Community Structure

2021 ◽  
Vol 11 (11) ◽  
pp. 5297
Author(s):  
Stavros D. Veresoglou ◽  
Leonie Grünfeld ◽  
Magkdi Mola
Keyword(s):  
Community Structure ◽  
Mycorrhizal Fungi ◽  
Root Colonization ◽  
Environmental Parameters ◽  
Arbuscular Mycorrhizal ◽  
Fungal Community Structure ◽  
High Connectivity ◽  
Spatio Temporal ◽  
Arbuscular Mycorrhizal Fungal ◽  
Colonization Rates

The roots of most plants host diverse assemblages of arbuscular mycorrhizal fungi (AMF), which benefit the plant hosts in diverse ways. Even though we understand that such AMF assemblages are non-random, we do not fully appreciate whether and how environmental settings can make them more or less predictable in time and space. Here we present results from three controlled experiments, where we manipulated two environmental parameters, habitat connectance and habitat quality, to address the degree to which plant roots in archipelagos of high connectivity and invariable habitats are colonized with (i) less diverse and (ii) easier to predict AMF assemblages. We observed no differences in diversity across our manipulations. We show, however, that mixing habitats and varying connectivity render AMF assemblages less predictable, which we could only detect within and not between our experimental units. We also demonstrate that none of our manipulations favoured any specific AMF taxa. We present here evidence that the community structure of AMF is less responsive to spatio-temporal manipulations than root colonization rates which is a facet of the symbiosis which we currently poorly understand.

Microbial diversity of soda lakes

Extremophiles ◽  
1998 ◽  
Vol 2 (3) ◽  
pp. 191-200 ◽  
Author(s):  
B. E. Jones ◽  
William D. Grant ◽  
A. W. Duckworth ◽  
G. G. Owenson
Keyword(s):  
Microbial Diversity ◽  
Soda Lakes

scholarly journals Factors Influencing the Microbial Composition of Metalworking Fluids and Potential Implications for Machine Operator's Lung

2011 ◽  
Vol 78 (1) ◽  
pp. 34-41 ◽  
Author(s):  
Jean-Benjamin Murat ◽  
Frédéric Grenouillet ◽  
Gabriel Reboux ◽  
Emmanuelle Penven ◽  
Adam Batchili ◽  
...  
Keyword(s):  
Metal Cutting ◽  
Hypersensitivity Pneumonitis ◽  
Environmental Parameters ◽  
Metalworking Fluids ◽  
Microbial Composition ◽  
Gram Positive ◽  
Gram Negative ◽  
Content Type ◽  
Kinetics Of

ABSTRACTHypersensitivity pneumonitis, also known as “machine operator's lung” (MOL), has been related to microorganisms growing in metalworking fluids (MWFs), especiallyMycobacterium immunogenum. We aimed to (i) describe the microbiological contamination of MWFs and (ii) look for chemical, physical, and environmental parameters associated with variations in microbiological profiles. We microbiologically analyzed 180 MWF samples from nonautomotive plants (e.g., screw-machining or metal-cutting plants) in the Franche-Comté region in eastern France and 165 samples from three French automotive plants in which cases of MOL had been proven. Our results revealed two types of microbial biomes: the first was from the nonautomotive industry, showed predominantly Gram-negative rods (GNR), and was associated with a low risk of MOL, and the second came from the automotive industry that was affected by cases of MOL and showed predominantly Gram-positive rods (GPR). Traces ofM. immunogenumwere sporadically detected in the first type, while it was highly prevalent in the automotive sector, with up to 38% of samples testing positive. The use of chromium, nickel, or iron was associated with growth of Gram-negative rods; conversely, growth of Gram-positive rods was associated with the absence of these metals. Synthetic MWFs were more frequently sterile than emulsions. Vegetable oil-based emulsions were associated with GNR, while mineral ones were associated with GPR. Our results suggest that metal types and the nature of MWF play a part in MWF contamination, and this work shall be followed by furtherin vitrosimulation experiments on the kinetics of microbial populations, focusing on the phenomena of inhibition and synergy.

scholarly journals Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

mBio ◽  
2013 ◽  
Vol 4 (2) ◽  
Author(s):  
Jizhong Zhou ◽  
Wenzong Liu ◽  
Ye Deng ◽  
Yi-Huei Jiang ◽  
Kai Xue ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Diversity ◽  
Microbial Community Structure ◽  
Community Assembly ◽  
Ecosystem Functioning ◽  
Dominant Role ◽  
Microbial Biodiversity ◽  
Stochastic Assembly

ABSTRACTThe processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management.IMPORTANCEMicroorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.

Sign in / Sign up

Export Citation Format

Share Document