Effects of agricultural soil management practices on soil microbiota across Europe – investigations in seven long term field experiments

Traditionally, soil quality has been assessed through physical, chemical and biological properties without paying attention to soil biota and the different associated ecosystem services provided (Tyler, 2019). To fill that gap, the european BiodivERsA &#8220;SoilMan&#8221; project (Ecosystem services driven by the diversity of soil biota &#8211; understanding and management in agriculture) is focused on the relations among soil management, soil biodiversity, and ecosystem services, at seven different management gradients in agricultural long term observations (LTO&#8217;s) trials across Europe (France &#8220;SOERE-PROs EFELE&#8221; and &#8220;SOERE-ACBB Lusigan&#8221;, Romania &#8220;Turda&#8221;, Sweden &#8220;Angermanland&#8221; and &#8220;S&#228;by-Uppland&#8221;, Germany &#8220;Garte S&#252;d&#8221; and Spain &#8220;La Hampa&#8221;). Management gradients covered different tillage regimes (zero, minimum and conventional) and different crop rotations (crop types and duration).In the present study, we characterised the bacterial and fungal communities of soils from the different countries and agricultural managements in arable land. The samplings were carried out following the same methodology in all the countries during 2017-2018 when wheat was sown in the LTO&#8217;s. The soil DNA was extracted and subjected to metabarcoding analysis of 16S and Internal Transcribed Spacer (ITS) ribosomal RNA (rRNA) for bacterial and fungal community analysis, respectively.Different alpha diversity metrics, including number of OTUs, Simpsons and Shannon indexes, as well as beta diversity distances (weighted and unweighted UNIFRAC, Jaccard and Bray-Curtis) were calculated. Multidimensional Scaling ordination plots (PCoA) were used to visualize the existence of community gradients among locations and soil managements. All the statistical data&#160; procedure&#160; was analysed using the vegan R package (Oksanen, 2011).In general terms, results show that alpha diversity for both bacteria and fungi, clearly differs among countries while soil management effects are less defined among and within countries. Concerning the beta diversity indexes, communities tend to cluster more according to the spatial location than due to the soil management regimen. This is especially true for fungal communities. Further analysis will identify possible correlations of bacterial and fungal communities with environmental variables and other physicochemical and biological soil properties.References:Oksanen, J. (2011). Multivariate Analysis of Ecological Communities in R: vegan tutorial.Tyler, H. L. (2019). Bacterial community composition under long-term reduced tillage and no till management. Journal of Applied Microbiology, 126(6), 1797&#8211;1807. https://doi.org/10.1111/jam.14267

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Effect of Long-Term Soil Management Practices on Tree Growth, Yield and Soil Biodiversity in a High-Density Olive Agro-Ecosystem

Agronomy ◽

10.3390/agronomy11061036 ◽

2021 ◽

Vol 11 (6) ◽

pp. 1036

Author(s):

Sauro Simoni ◽

Giovanni Caruso ◽

Nadia Vignozzi ◽

Riccardo Gucci ◽

Giuseppe Valboa ◽

...

Keyword(s):

Organic Carbon ◽

Soil Organic Carbon ◽

Soil Structure ◽

Soil Management ◽

Carbon Pools ◽

Grass Cover ◽

Soil Biodiversity ◽

Canopy Effect ◽

Soil Organic Carbon Pools

Edaphic arthropod communities provide valuable information about the prevailing status of soil quality to improve the functionality and long-term sustainability of soil management. The study aimed at evaluating the effect of plant and grass cover on the functional biodiversity and soil characteristics in a mature olive orchard (Olea europaea L.) managed for ten years by two conservation soil managements: natural grass cover (NC) and conservation tillage (CT). The trees under CT grew and yielded more than those under NC during the period of increasing yields (years 4–7) but not when they reached full production. Soil management did not affect the tree root density. Collecting samples underneath the canopy (UC) and in the inter-row space (IR), the edaphic environment was characterized by soil structure, hydrological properties, the concentration and storage of soil organic carbon pools and the distribution of microarthropod communities. The soil organic carbon pools (total and humified) were negatively affected by minimum tillage in IR, but not UC, without a loss in fruit and oil yield. The assemblages of microarthropods benefited, firstly, from the grass cover, secondly, from the canopy effect, and thirdly, from a soil structure ensuring a high air capacity and water storage. Feeding functional groups—hemiedaphic macrosaprophages, polyphages and predators—resulted in selecting the ecotonal microenvironment between the surface and edaphic habitat.

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Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

10.7287/peerj.preprints.27887 ◽

2019 ◽

Cited By ~ 1

Author(s):

Ze Ren ◽

Hongkai Gao

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Central Asia ◽

Fungal Community ◽

Bacterial Communities ◽

Beta Diversity ◽

Hydrological Modeling ◽

Alpha Diversity ◽

Environmental Variation ◽

Fungal Communities

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of bacterial community and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while fungal community and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

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Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

10.7287/peerj.preprints.27887v1 ◽

2019 ◽

Author(s):

Ze Ren ◽

Hongkai Gao

Keyword(s):

Bacterial Community ◽

Microbial Communities ◽

Central Asia ◽

Fungal Community ◽

Bacterial Communities ◽

Beta Diversity ◽

Hydrological Modeling ◽

Alpha Diversity ◽

Environmental Variation ◽

Fungal Communities

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Impact of Early Life Antibiotic Exposure and Neonatal Hyperoxia on the Murine Microbiome and Lung Injury

Scientific Reports ◽

10.1038/s41598-019-51506-0 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

Melissa H. Althouse ◽

Christopher Stewart ◽

Weiwu Jiang ◽

Bhagavatula Moorthy ◽

Krithika Lingappan

Keyword(s):

Lung Injury ◽

Beta Diversity ◽

Alpha Diversity ◽

Intestinal Microbiome ◽

Rrna Gene ◽

Antibiotic Exposure ◽

Neonatal Mice ◽

Intestinal Dysbiosis ◽

Neonatal Hyperoxia

Abstract Cross talk between the intestinal microbiome and the lung and its role in lung health remains unknown. Perinatal exposure to antibiotics disrupts the neonatal microbiome and may have an impact on the preterm lung. We hypothesized that perinatal antibiotic exposure leads to long-term intestinal dysbiosis and increased alveolar simplification in a murine hyperoxia model. Pregnant C57BL/6 wild type dams and neonatal mice were treated with antibiotics before and/or immediately after delivery. Control mice received phosphate-buffered saline (PBS). Neonatal mice were exposed to 95% oxygen for 4 days or room air. Microbiome analysis was performed using 16S rRNA gene sequencing. Pulmonary alveolarization and vascularization were analyzed at postnatal day (PND) 21. Perinatal antibiotic exposure modified intestinal beta diversity but not alpha diversity in neonatal mice. Neonatal hyperoxia exposure altered intestinal beta diversity and relative abundance of commensal bacteria in antibiotic treated mice. Hyperoxia disrupted pulmonary alveolarization and vascularization at PND 21; however, there were no differences in the degree of lung injury in antibiotic treated mice compared to vehicle treated controls. Our study suggests that exposure to both hyperoxia and antibiotics early in life may cause long-term alterations in the intestinal microbiome, but intestinal dysbiosis may not significantly influence neonatal hyperoxic lung injury.

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Corrigendum: Effects of Short- and Long-Term Variation in Resource Conditions on Soil Fungal Communities and Plant Responses to Soil Biota

Frontiers in Plant Science ◽

10.3389/fpls.2018.01937 ◽

2019 ◽

Vol 9 ◽

Author(s):

Philip G. Hahn ◽

Lorinda Bullington ◽

Beau Larkin ◽

Kelly LaFlamme ◽

John L. Maron ◽

...

Keyword(s):

Soil Biota ◽

Fungal Communities ◽

Plant Responses ◽

Term Variation ◽

Short And Long Term ◽

Resource Conditions

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Ecological networks reveal contrasting patterns of bacterial and fungal communities in glacier-fed streams in Central Asia

PeerJ ◽

10.7717/peerj.7715 ◽

2019 ◽

Vol 7 ◽

pp. e7715 ◽

Cited By ~ 2

Author(s):

Ze Ren ◽

Hongkai Gao

Keyword(s):

Microbial Communities ◽

Central Asia ◽

Bacterial Communities ◽

Beta Diversity ◽

Vegetation Index ◽

Hydrological Modeling ◽

Alpha Diversity ◽

Environmental Variation ◽

Fungal Communities ◽

Taxonomic Groups

Bacterial and fungal communities in biofilms are important components in driving biogeochemical processes in stream ecosystems. Previous studies have well documented the patterns of bacterial alpha diversity in stream biofilms in glacier-fed streams, where, however, beta diversity of the microbial communities has received much less attention especially considering both bacterial and fungal communities. A focus on beta diversity can provide insights into the mechanisms driving community changes associated to large environmental fluctuations and disturbances, such as in glacier-fed streams. Moreover, modularity of co-occurrence networks can reveal more ecological and evolutionary properties of microbial communities beyond taxonomic groups. Here, integrating beta diversity and co-occurrence approach, we explored the network topology and modularity of the bacterial and fungal communities with consideration of environmental variation in glacier-fed streams in Central Asia. Combining results from hydrological modeling and normalized difference of vegetation index, this study highlighted that hydrological variables and vegetation status are major variables determining the environmental heterogeneity of glacier-fed streams. Bacterial communities formed a more complex and connected network, while the fungal communities formed a more clustered network. Moreover, the strong interrelations among the taxonomic dissimilarities of bacterial community (BC) and modules suggest they had common processes in driving diversity and taxonomic compositions across the heterogeneous environment. In contrast, fungal community (FC) and modules generally showed distinct driving processes to each other. Moreover, bacterial and fungal communities also had different driving processes. Furthermore, the variation of BC and modules were strongly correlated with hydrological properties and vegetation status but not with nutrients, while FC and modules (except one module) were not associated with environmental variation. Our results suggest that bacterial and fungal communities had distinct mechanisms in structuring microbial networks, and environmental variation had strong influences on bacterial communities but not on fungal communities. The fungal communities have unique assembly mechanisms and physiological properties which might lead to their insensitive responses to environmental variations compared to bacterial communities. Overall, beyond alpha diversity in previous studies, these results add our knowledge that bacterial and fungal communities have contrasting assembly mechanisms and respond differently to environmental variation in glacier-fed streams.

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Sheltering Role of Well-Decayed Conifer Logs for Forest Floor Fungi in Long-Term Polluted Boreal Forests

Frontiers in Microbiology ◽

10.3389/fmicb.2021.729244 ◽

2021 ◽

Vol 12 ◽

Author(s):

Vladimir S. Mikryukov ◽

Olesya V. Dulya ◽

Igor E. Bergman ◽

Georgiy A. Lihodeevskiy ◽

Anzhelika D. Loginova ◽

...

Keyword(s):

Boreal Forests ◽

Fungal Diversity ◽

Woody Debris ◽

Alpha Diversity ◽

Forest Litter ◽

Forest Degradation ◽

Fungal Communities ◽

Low Rank ◽

Industrial Emissions

Coarse woody debris (CWD) provides food and shelter to a large proportion of forest biota and is considered vital for biodiversity during periods of harsh weather. However, its importance in long-term stressed ecosystems remains largely unknown. In this work, we explored the contribution of CWD to fungal diversity along the gradient of boreal forest degradation caused by 77 years of heavy industrial emissions. We analyzed the diversity and composition of fungi in 270 samples of well-decayed Picea abies and Abies sibirica logs, as well as forest litter both adjacent to and distant from the logs. Compared with forest litter, the wood had higher water content and possessed substantially lower concentrations of heavy metals, which suggests its potential favorability for biota in polluted areas. The pollution-induced loss of fungal diversity in forest litter reached 34% and was stronger in the microhabitats not influenced by CWD. Meanwhile, wood fungal communities lost less than 10% of their total richness and even increased in alpha diversity. These processes led to the diversity and compositional convergence of fungal communities from different microhabitats and substrates in polluted areas. Despite this, the importance of wood and CWD-influenced microhabitats for fungal diversity maintenance was low. Apart from wood-associated fungi, the taxa whose diversity increased in the wood of polluted areas were ectomycorrhizal fungi and eurytopic soil saprotrophs (Mucoromycota, Mortierellomycota, Eurotiomycetes, and Helotiales) that easily tolerate highly toxic litter. Within the majority of pollution-sensitive soil saprotrophic groups, only terricolous Tricholomataceae benefit from CWD as microrefugia. Upon considering the ecological variability within low-rank taxa, the importance of decayed logs as safe sites can be high for certain soil-inhabiting fungal groups in polluted areas.

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Gut Microbiota Changes During Helicobacter Pylori Eradication with Vonoprazan-Containing Triple Therapy Among Adolescents: A Prospective Multicenter Study in Japan

10.21203/rs.3.rs-37210/v1 ◽

2020 ◽

Author(s):

Toshihiko kakiuchi ◽

Kentaroh Yamamoto ◽

Ichiro Imamura ◽

Kazutoshi Hashiguchi ◽

Hiroharu Kawakubo ◽

...

Keyword(s):

Helicobacter Pylori ◽

Gut Microbiota ◽

Beta Diversity ◽

Medical Information ◽

Eradication Therapy ◽

Alpha Diversity ◽

University Hospital ◽

Healthy Children ◽

Serious Adverse Events

Abstract Background: Whether the screening and treatment of Helicobacter pylori infection are safe for children is debated in Japan. This study aimed to evaluate the safety of Helicobacter pylori eradication therapy by examining long-term changes in the gut microbiota during therapy among children.Methods: Children with anti-Helicobacter pylori antibody in the urine and Helicobacter pylori antigen in the feces were enrolled in this study. Their stool samples were collected at three time points, which were as follows: prior to treatment, 1–2 days after treatment, and time of judgment of eradication therapy. After treatment, the relative abundance, alpha-diversity, and beta-diversity of the gut microbiota were assessed.Results: In 16 students finally included in the study, the number of Actinobacteria isolated decreased immediately after eradication therapy, and it returned to pretreatment condition at the judgment point. There was no change at the genus level. The alpha-diversity was lost immediately after eradication therapy. However, it recovered at the time of eradication judgment, and it was restored before eradication therapy. Meanwhile, there was no change in beta-diversity, and none of the participants experienced serious adverse events.Conclusion: Helicobacter pylori eradication therapy is safe even for children in the view point of gut microbiota. Thus, further long-term evaluations of changes in the gut microbiota after eradication therapy and an assessment of healthy children without Helicobacter pylori must be performed. These will in turn promote screening and treatment among adolescents to prevent gastric cancer.Trial registration: This study was registered with the University Hospital Medical Information Network Clinical Trials Registry (no. UMIN000028726, https://upload.umin.ac.jp/cgi-bin/ctr_e/ctr_view.cgi?recptno=R000032873) on 18 August 2017.

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Conventional agriculture and not drought alters relationships between soil biota and functions

Scientific Reports ◽

10.1038/s41598-021-03276-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Klaus Birkhofer ◽

Andreas Fliessbach ◽

María Pilar Gavín-Centol ◽

Katarina Hedlund ◽

María Ingimarsdóttir ◽

...

Keyword(s):

Agricultural Practices ◽

Growing Season ◽

Significant Loss ◽

Climatic Conditions ◽

Soil Biota ◽

Ecosystem Functions ◽

Conventional Farming ◽

Soil Biodiversity ◽

Conventional Agriculture

AbstractSoil biodiversity constitutes the biological pillars of ecosystem services provided by soils worldwide. Soil life is threatened by intense agricultural management and shifts in climatic conditions as two important global change drivers which are not often jointly studied under field conditions. We addressed the effects of experimental short-term drought over the wheat growing season on soil organisms and ecosystem functions under organic and conventional farming in a Swiss long term trial. Our results suggest that activity and community metrics are suitable indicators for drought stress while microbial communities primarily responded to agricultural practices. Importantly, we found a significant loss of multiple pairwise positive and negative relationships between soil biota and process-related variables in response to conventional farming, but not in response to experimental drought. These results suggest a considerable weakening of the contribution of soil biota to ecosystem functions under long-term conventional agriculture. Independent of the farming system, experimental and seasonal (ambient) drought conditions directly affected soil biota and activity. A higher soil water content during early and intermediate stages of the growing season and a high number of significant relationships between soil biota to ecosystem functions suggest that organic farming provides a buffer against drought effects.

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