scholarly journals Soil detrital inputs increase stimulate bacterial saprotrophs with different timing and intensity compared to fungal saprotrophs

2018 ◽  
Author(s):  
Nicole Sukdeo ◽  
Ewing Teen ◽  
P. Michael Rutherford ◽  
Hugues B. Massicotte ◽  
Keith N. Egger
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Community Composition ◽  
Mineral Soil ◽  
Ecosystem Functions ◽  
Soil Reclamation ◽  
Activity Levels ◽  
Fungal Community Composition ◽  
And Shifts

AbstractSoils contain microbial inhabitants that differ in sensitivity to anthropogenic modification. Soil reclamation relies on monitoring these communities to evaluate ecosystem functions recovery post-disturbance. DNA metabarcoding and soil enzyme assays provide information about microbial functional guilds and organic matter decomposition activities respectively. However bacterial communities, fungal communities, and enzyme activities may not be equally informative for monitoring reclaimed soils. We compared effects of disturbance regimes applied to forest soils on fungal community composition, bacterial community composition, and potential hydrolase activities (N-acetyl-β-D-glucosaminidase, acid phosphatase, and cellobiohydrolase) at two times (14 days and 5 months post-disturbance) and depths (LFH versus mineral soil). Using disturbance versus control comparisons allowed us to identify genus-level disturbance-indicators and shifts in hydrolase activity levels. We observed declines in disturbed LFH fungal biomass (ergosterol) and declines in ectomycorrhizal fungi abundance across all disturbed samples, which prompted us to consider necromass-induced (fungal, root) saprotroph increases as disturbance indicators. Fungal community composition strongly shifted away from ecotmycorrhizal dominance to saprotroph dominance (i.e. increasedMortierella, andUmbelopsis) in disturbed plots at 5 months, while bacterial community composition did not shift to distinguish control plots from disturbed ones at either sampling time. Soil potential hydrolase data mainly indicated that mixing LFH material into mineral soil increases the measured activity levels compared to control and replaced mineral soil. Bacterial saprotrophs previously associated with mycelial necromass were detected across multiple regimes as disturbance indicators at 14 days post-disturbance. Our results confirm that ectomycorrhizal fungal genera are sensitive and persistently impacted by soil physical disturbances. Increases in saprotrophic bacterial genera are detectable 14 days pot-disturbance but only a few persist as disturbance indicators after several months. Potential hydrolase activities appear to be most useful for detecting the transfer of decomposition hotspots into mineral soils.

scholarly journals Differential mechanisms underlying responses of soil bacterial and fungal communities to nitrogen and phosphorus inputs in a subtropical forest

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e7631 ◽  
Author(s):  
Yong Li ◽  
Dashuan Tian ◽  
Jinsong Wang ◽  
Shuli Niu ◽  
Jing Tian ◽  
...  
Keyword(s):  
Species Richness ◽  
Bacterial Community ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Community Composition ◽  
Shannon Index ◽  
Subtropical Forest ◽  
Fungal Community Composition ◽  
Soil Bacterial ◽  
P Addition

Atmospheric nitrogen (N) deposition and phosphorus (P) addition both can change soil bacterial and fungal community structure with a consequent impact on ecosystem functions. However, which factor plays an important role in regulating responses of bacterial and fungal community to N and P enrichments remains unclear. We conducted a manipulative experiment to simulate N and P inputs (10 g N · m−2 · yr−1 NH4NO3 or 10 g P · m−2 · yr−1 NaH2PO4) and compared their effects on soil bacterial and fungal species richness and community composition. The results showed that the addition of N significantly increased NH4+ and Al3+ by 99.6% and 57.4%, respectively, and consequently led to a decline in soil pH from 4.18 to 3.75 after a 5-year treatment. P addition increased Al3+ and available P by 27.0% and 10-fold, respectively, but had no effect on soil pH. N addition significantly decreased bacterial species richness and Shannon index and resulted in a substantial shift of bacterial community composition, whereas P addition did not. Neither N nor P addition changed fungal species richness, Shannon index, and fungal community composition. A structural equation model showed that the shift in bacterial community composition was related to an increase in soil acid cations. The principal component scores of soil nutrients showed a significantly positive relationship with fungal community composition. Our results suggest that N and P additions affect soil bacterial and fungal communities in different ways in subtropical forest. These findings highlight how the diversity of microbial communities of subtropical forest soil will depend on future scenarios of anthropogenic N deposition and P enrichment, with a particular sensitivity of bacterial community to N addition.

scholarly journals Long-Term Fertilization Affects Soil Microbiota, Improves Yield and Benefits Soil

Agronomy ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1664
Author(s):  
Felix R. Kurzemann ◽  
Ulrich Plieger ◽  
Maraike Probst ◽  
Heide Spiegel ◽  
Taru Sandén ◽  
...  
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Bacterial Community Composition ◽  
Farmyard Manure ◽  
Maize Yield ◽  
N Fertilizer ◽  
Fungal Community Composition ◽  
Mineral N ◽  
Soil Microbiota

Fertilization of soil is needed to fulfill the growing demand for livestock feed and human food requirements. However, fertilization has short and long-term impacts on the soil microbiota. These, in turn, may influence plant viability and growth. We investigated the soil microbiota of a 27-year field trial, focusing on the influences of mineral nitrogen (N) fertilization, different composts and combinations of compost plus mineral N as soil amendments. Two N rates (0 and 80 kg per ha) and four different composts (urban organic waste compost (OWC) green waste compost (GC), farmyard manure (MC) compost and sewage sludge compost (SSC)) were used. Soil samples for this study were taken in 2018 after the growing season of maize. In addition to maize yield, the effects on soil physicochemical properties and the soil microbiota were analyzed. There was a trend for increased maize yields for all fertilizers; however, only the application of GC and SSC in combination with mineral N fertilizer showed significant effects. The different organic amendments influenced physicochemical soil properties. Phosphorus concentrations were three times higher in plots receiving SSC (≈312 mg kg−1) and SSC + N (≈297 mg kg−1) than control (≈89 mg kg−1) or mineral N fertilizer (≈97 mg kg−1) alone. Magnesium concentrations in plots treated with SSC (≈74 mg kg−1) were lower compared to soils treated with GC and MC, respectively (≈135 mg kg−1 and 126 mg kg−1). Bacteria exceeded the fungal community in terms of both richness and diversity. While the bacterial community composition differed significantly among the treatments, the fungal community composition was rather unaffected. Our conclusion is that composts produced from various substrates serve as valuable nutrient sources for plants and can partially substitute mineral N. In addition, composts increased soil microbial biomass and modulated the composition of the soil’s microbial community.

scholarly journals Machine learning for exploring microbial inter-kingdom associations in Cystic Fibrosis and Bronchiectasis

2022 ◽  
Author(s):  
Leah Cuthbertson ◽  
Jonathan Ish-horowicz ◽  
Imogen Felton ◽  
Phillip James ◽  
Elena Turek ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cystic Fibrosis ◽  
Community Composition ◽  
Fungal Community ◽  
Bacterial Communities ◽  
Bacterial Community Composition ◽  
Disease Status ◽  
Fungal Disease ◽  
Rrna Gene ◽  
Fungal Community Composition

Background: Cystic fibrosis (CF) and non-CF bronchiectasis (BX) are lung diseases characterised by severe chronic infections. Fungal and bacterial components of infection are both recognized. Recent molecular investigation of sputum from patients with CF and BX has revealed a complex mycobiome. However, little is known about how fungal and bacterial organisms interact or whether the interactions impact on disease outcomes. Methods: Quantitative PCR and next generation sequencing of ITS2 and 16S rRNA gene was carried out on 107 patients with CF and BX and defined clinical fungal infection status. Fungal and bacterial communities were explored using supervised and unsupervised machine learning to understand associations between fungal and bacterial communities and their relationship to disease. Results: Fungal and bacterial communities both had significantly higher biomass and lower diversity in CF compared to BX patients. Random forest modelling demonstrated that the fungal and bacterial communities were distinct between CF and BX patients. Within the CF group, bacterial communities contained no predictive signal for fungal disease status. Neither bacterial nor fungal community composition were predictive of the presence of CF pulmonary exacerbation (CFPE). Intra-kingdom correlations were far stronger than those between the two kingdoms. Dirichlet mixture components analysis identified two distinct clusters of bacteria related to the relative abundance of Pseudomonas. Fungal community composition contained no predictive signal for bacterial clusters. Conclusions: Clear changes in diversity were observed between patients with different clinical disease status. Although our results demonstrate that bacterial community composition differs in the presence of fungal disease, no direct relationship between bacterial and fungal OTUs was found.

Changes in bacterial community composition across natural grassland and pine forests in the Bunya Mountains in subtropical Australia

Soil Research ◽  
2019 ◽  
Vol 57 (8) ◽  
pp. 825
Author(s):  
Ju-Pei Shen ◽  
Maryam Esfandbod ◽  
Steve A. Wakelin ◽  
Gary Bacon ◽  
Qiaoyun Huang ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Bacterial Community Composition ◽  
Pine Forest ◽  
Ecosystem Functions ◽  
C3 Plants ◽  
Α Diversity ◽  
Eastern Australia ◽  
Hoop Pine ◽  
Subtropical Australia

Tree and grass species coexist in many ecosystems worldwide and support multiple ecosystem functions and services. However, the distribution of bacterial communities and factors driving coexistence in tree–grass associations and their ecosystem functions remain poorly understood. In this study, the distribution of soil bacteria and their link to changes in abiotic factors were investigated in adjacent montane grassland (C4 plants) and pine forest (bunya pine and hoop pine; C3 plants) sites in the Bunya Mountains, subtropical Australia. Different vegetation (grassy balds and forest) had a substantial effect on terrestrial ecosystem properties, with higher levels of soil nutrients (e.g. total nitrogen (N), total phosphorus (P)) and electrical conductivity (EC), and lower δ13C values and pH under forests compared with grassland. Bacterial α-diversity (total species per operational taxonomic unit richness) did not differ between grassland and pine forest sites, whereas strong shifts in the bacterial community composition and structure were evident. Patterns in bacterial community structure were strongly associated with changes in soil pH, EC, total P and δ13C. Different bacterial groups associated with pine forest (Gammaproteobacteria and Alphaproteobacteria) and grassland (Acidobacteria and Verrucomicrobia) were identified as key groups contributing to the segregation of these two ecosystems in the Bunya Mountains. These findings suggest that heterogeneity in soil edaphic properties (e.g. key nutrients) likely contributed to variation in bacterial β-diversity of grassland and pine forest, which has potential implications for species coexistence and ecosystem function in montane eastern Australia.

scholarly journals Preferential associations of soil fungal taxa under mixed compositions of eastern American tree species

2021 ◽  
Author(s):  
Steve Kutos ◽  
Elle M. Barnes ◽  
Arnav Bhutada ◽  
JD Lewis
Keyword(s):  
Community Composition ◽  
Fungal Community ◽  
Tree Species ◽  
Soil Microbial Communities ◽  
Acer Rubrum ◽  
Fungal Communities ◽  
Ecosystem Functions ◽  
Relative Role ◽  
Fungal Community Composition ◽  
Functional Changes

Soil fungi are vital to forest ecosystem functions, in part through their role mediating tree responses to environmental factors, as well as directly through effects on resource cycling. While the distribution of these key taxa may vary with a suite of abiotic and biotic factors, the relative role of host species identity on soil fungal community composition and function remains unresolved. In this study, we used a combination of amplicon sequencing and enzymatic assays to assess soil fungal composition and associated function under three tree species, Quercus rubra, Betula nigra, and Acer rubrum, planted individually and in all combinations in a greenhouse, with added fungal inoculum collected below mature field trees. Across treatments, fungal communities were dominated by the phylum Ascomycota, followed by Basidiomycota and Mortierellomycota. Nonetheless, fungal communities differed between each of the solo planted treatments, suggesting at least some taxa may associate preferentially with these tree species. Additionally, fungal community composition under mixed sapling treatments broadly differed from solo saplings. The data also suggests that there were larger enzymatic activities in the solo treatments as compared with all mixed treatments. This difference may be due to the greater relative abundance of saprobic taxa found in the solo treatments. This study provides evidence of the importance of tree identity on soil microbial communities and functional changes to forest soils.

scholarly journals Collection of Environmental Variables and Bacterial Community Compositions in Marian Cove, Antarctica, during Summer 2018

Data ◽  
2021 ◽  
Vol 6 (3) ◽  
pp. 27
Author(s):  
Hyo-Ryeon Kim ◽  
Jae-Hyun Lim ◽  
Ju-Hyoung Kim ◽  
Il-Nam Kim
Keyword(s):  
Bacterial Community ◽  
Community Composition ◽  
Marine Bacteria ◽  
Environmental Variables ◽  
Environmental Changes ◽  
Bacterial Community Composition ◽  
Composition Data ◽  
Decomposition Of Organic Matter ◽  
Class Level ◽  
Earth’S Climate

Marine bacteria, which are known as key drivers for marine biogeochemical cycles and Earth’s climate system, are mainly responsible for the decomposition of organic matter and production of climate-relevant gases (i.e., CO₂, N₂O, and CH₄). However, research is still required to fully understand the correlation between environmental variables and bacteria community composition. Marine bacteria living in the Marian Cove, where the inflow of freshwater has been rapidly increasing due to substantial glacial retreat, must be undergoing significant environmental changes. During the summer of 2018, we conducted a hydrographic survey to collect environmental variables and bacterial community composition data at three different layers (i.e., the seawater surface, middle, and bottom layers) from 15 stations. Of all the bacterial data, 17 different phylum level bacteria and 21 different class level bacteria were found and Proteobacteria occupy 50.3% at phylum level following Bacteroidetes. Gammaproteobacteria and Alphaproteobacteria, which belong to Proteobacteria, are the highest proportion at the class level. Gammaproteobacteria showed the highest relative abundance in all three seawater layers. The collection of environmental variables and bacterial composition data contributes to improving our understanding of the significant relationships between marine Antarctic regions and marine bacteria that lives in the Antarctic.

scholarly journals Artificial neural network analysis of microbial diversity in the central and southern Adriatic Sea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Danijela Šantić ◽  
Kasia Piwosz ◽  
Frano Matić ◽  
Ana Vrdoljak Tomaš ◽  
Jasna Arapov ◽  
...  
Keyword(s):  
Neural Network ◽  
Network Analysis ◽  
Bacterial Community ◽  
Microbial Diversity ◽  
Community Composition ◽  
Adriatic Sea ◽  
Bacterial Community Composition ◽  
Environmental Data ◽  
Large Contribution ◽  
Neural Network Analysis

AbstractBacteria are an active and diverse component of pelagic communities. The identification of main factors governing microbial diversity and spatial distribution requires advanced mathematical analyses. Here, the bacterial community composition was analysed, along with a depth profile, in the open Adriatic Sea using amplicon sequencing of bacterial 16S rRNA and the Neural gas algorithm. The performed analysis classified the sample into four best matching units representing heterogenic patterns of the bacterial community composition. The observed parameters were more differentiated by depth than by area, with temperature and identified salinity as important environmental variables. The highest diversity was observed at the deep chlorophyll maximum, while bacterial abundance and production peaked in the upper layers. The most of the identified genera belonged to Proteobacteria, with uncultured AEGEAN-169 and SAR116 lineages being dominant Alphaproteobacteria, and OM60 (NOR5) and SAR86 being dominant Gammaproteobacteria. Marine Synechococcus and Cyanobium-related species were predominant in the shallow layer, while Prochlorococcus MIT 9313 formed a higher portion below 50 m depth. Bacteroidota were represented mostly by uncultured lineages (NS4, NS5 and NS9 marine lineages). In contrast, Actinobacteriota were dominated by a candidatus genus Ca. Actinomarina. A large contribution of Nitrospinae was evident at the deepest investigated layer. Our results document that neural network analysis of environmental data may provide a novel insight into factors affecting picoplankton in the open sea environment.

Sign in / Sign up

Export Citation Format

Share Document