Soil microbial responses to passive restoration strategies in drylands: a temporal comparison of soil biodiversity and ecosystem function

2021 ◽  
Author(s):  
Jana Stewart ◽  
Nathali Machado de Lima ◽  
Richard Kingsford ◽  
Miriam Muñoz-Rojas
Keyword(s):  
Climate Change ◽  
Environmental Indicators ◽  
Ecosystem Functions ◽  
Rrna Gene ◽  
Research Station ◽  
Microbial Composition ◽  
Soil Biodiversity ◽  
Passive Restoration ◽  
The Impact ◽  
Over Time

<p>Arid and semi-arid (from hereafter dryland) ecosystems cover 70% of Australia, with climate change set to increase this area through desertification. Increased temperatures and reduced water availability are compounded through agricultural overgrazing. This degradation and habitat loss has led to biodiversity loss which disrupts the biogeochemical cycles that maintain these environments, creating a negative feedback loop, and making restoration efforts largely unsuccessful. With soil microbes being important drivers in dryland systems, understanding how different stressors impact the soil biome is needed to improve conservation and restoration efforts and promote resilience and resistance to climate change. Particularly lacking is understanding of these interactions over time.</p><p>Fowlers Gap Research Station is the only research station in the arid zone of Australia and was a working sheep station until 2019. Due to agricultural overgrazing the site is largely degraded however exclusion zones have been set up on the property ranging in time from 3 years to 40 years. These exclusion zones provide a powerful comparison for the impact of soil degradation on drylands. To investigate the impact of overgrazing on the soil biodiversity and ecosystem functions, we selected three of the exclusion zones paired with three degraded sites directly outside of the exclusion zone to assess their microbial composition and functional diversity, along with soil physicochemical properties. We aim to build 16S rRNA gene libraries and co-relate them with the soil chemical variables, to assess the impact of overgrazing on these microbial communities and the ecosystem functions they provide. This knowledge can be used to improve monitoring of conservation and restoration initiatives by providing environmental indicators for soil health over time.</p>

Bushfire impacts on a threatened swamp ecosystem: responses of the soil microbial communities and restoration

2021 ◽  
Author(s):  
Nathali Machado de Lima ◽  
Alexandria Thomsen ◽  
Mark Ooi ◽  
Miriam Muñoz-Rojas
Keyword(s):  
Microbial Communities ◽  
Longwall Mining ◽  
Soil Microbial Communities ◽  
Environmental Indicators ◽  
Fire Season ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Drought Period ◽  
Soil Microbial ◽  
The Impact

<p>Australia faced the most extreme and prolonged fire season in 2019-2020, resulting in tragic habitat loss for many threatened species and the destruction of many ecological communities.  Newnes Plateau Shrub Swamps are peatlands located in the upper Blue Mountains region of New South Wales, Australia. These ecosystems perform many important ecological functions while absorbing and filtering water and releasing it slowly back to the environment. Their functions are related to the control of peak flow events, water purification and the harboring of many threatened plant and animal species. Despite their ecological importance, the area has been intensively degraded through longwall mining processes, resulting in the lowering and loss of water tables in the area. In December 2019 these impacts were compounded by an intense prolonged drought period and extensive wildfire. While the effects of these combined factors on the vegetation have been analysed and revealed remarkable negative impacts in the swamps under mining pressures, the effects on the soil microbial communities and related soil functions have not yet been studied. To investigate both drivers (fire and mining activities), we selected three mined swamps and three unmined swamps to assess their soil microbial composition and diversity through Next Generation Sequencing, and to characterise the soil chemical composition. At each site, we collected samples considering three treatments, one in the swamp valley fill and two at two different heights of the swamp valley margin, focusing on the soil close to specific groups of plants (e.g. sedges and shrubs). For each site and treatment, three soil samples (~ 10 m from each other) of 10x10 cm and ~ 3 to 5 cm of depth were collected using a trowel. We aim to build 16S rRNA gene libraries and co-relate them with the soil chemical variables, to assess the impact on these microbial communities and their possible use as environmental indicators and basis for future applied initiatives in conservation and restoration.</p><p> </p>

scholarly journals FOREST CERTIFICATION AS A TOOL TO ENSURE THE BALANCE OF FORESTRY LAND USE

2021 ◽  
Vol 71 (3) ◽  
Author(s):  
Stepan Dankevych
Keyword(s):  
Land Use ◽  
Regional Scale ◽  
Environmental Indicators ◽  
Statistical Characteristics ◽  
Forest Certification ◽  
Capital Investments ◽  
Forest Lands ◽  
The Impact ◽  
The Relationship ◽  
Over Time

The problem of ensuring the balanced use of forest lands determines the search for new economic and environmental tools that can influence this process. The need to improve the certification tool as part of the financial and economic mechanism for ensuring balanced forestry land use corresponds to the directions of state policy and European integration intentions of Ukraine, modern requirements of the ecological aspect of forestry land use. The work examines the practice in the field of forest certification in Ukraine from the point of view of balanced land use. Spatial-temporal analysis and assessment of the scale and dynamics of the spread of forest FSC certification in Ukraine has been carried out. The study was formed in three stages: (I) study of changes over time in the volume of forest certification on a national scale, (II) assessment of trends over time for indicators on a regional scale, (III) study of the relationship between individual indicators. The analysis of the impact of FSC-certification of forest management in Ukraine on the environmental indicators of forestry land use based on the results of the correlation between the statistical characteristics of certain economic and environmental indicators, such as the area of certified forests, capital investments, reforestation. Analysis of statistical data showed the relationship between environmental and economic performance over time and changes in specific characteristics on a regional scale. The study makes it possible, on the basis of an objectively existing causal relationship between phenomena and indicators, to identify the course of certain positive or negative processes in forestry land use. Forest certification can play a role in maintaining a balanced use of forest lands, preventing illegal logging, forest degradation and contributing to reforestation and capital investments. The study helps to identify certain key variables that limit the ability of forestry operators to ensure balanced use of forest lands and how forest certification can affect this. Foreign experience in stimulating forest certification has been investigated for the possibility of borrowing the experience of using management tools in order to motivate forest certification in Ukraine. It has been proven that certification is a significant environmental tool for ensuring a balanced level of land use and has the potential for further development.

scholarly journals Influence of Agaricus Bisporus Establishment and Fungicidal Treatments on Casing Soil Metataxonomy During Mushroom Cultivation

2021 ◽  
Author(s):  
Maria Luisa Tello ◽  
Rebeca Lavega ◽  
Margarita Pérez ◽  
Antonio J. Pérez ◽  
Michael Thon ◽  
...  
Keyword(s):  
Agaricus Bisporus ◽  
Illumina Miseq ◽  
Biological Efficiency ◽  
Its2 Region ◽  
Rrna Gene ◽  
Mushroom Cultivation ◽  
Microbial Composition ◽  
Mycelium Growth ◽  
Bacterial Phyla ◽  
The Impact

Abstract The cultivation of edible mushroom is an emerging sector with a potential yet to be discovered. Unlike plants, it is a less developed agriculture where many studies are lacking to optimize the cultivation. Mushrooms are a source of resources still to be revealed, which have applications not only in food, but in many other sectors such as health, industry and biotechnology. Mushroom cultivation consists of the development of selective substrates through composting where the mushroom grows via solid fermentation process. In case of Agaricus bisporus, the compost fully colonized by mycelium hardly produces mushrooms and it is necessary to apply a casing layer with certain physical, chemical and biological characteristics to shift from the vegetative mycelium to the reproductive one, where the native microbiota plays crucial roles. Currently, the industry faces a challenge to substitute the actual peat based casing materials due to the limited natural resources and the impact on the peatlands where peat is extracted.In this work we have employed high-throughput techniques by next generation sequencing to screen the microbial structure of casing soil employed in mushroom cultivation while sequencing V3-V4 of the 16S rRNA gene for bacteria and the ITS2 region of rRNA for fungi in an Illumina MiSeq. In addition, the microbiome dynamics and evolution (bacterial and fungal communities) in peat based casing along the process of incubation of Agaricus bisporus have been studied, while comparing the effect of fungicidal treatment (Chlorothalonil and Metrafenone). Statistically significant changes in populations of bacteria and fungi were observed. Microbial composition differed significantly based on incubation day, changing radically from the original communities to a specific microbial composition adapted to enhance the A. bisporus mycelium growth. Chlorothalonil treatment seems to delay casing colonization by A. bisporus. Proteobacteria and Bacteroidota appeared as the most dominant bacterial phyla. We observed a great change in the structure of the bacteria populations between day 0 and the following days. Fungi populations changed more gradually, A. bisporus displacing the rest of the species as the cultivation cycle progresses. A better understanding of the microbial communities in the casing will hopefully allow us to increase the biological efficiency during production as well as possibly help us to have a clearer view of the microbial community-pathogen relationships as they are directly related to disease development.

scholarly journals Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans

mSphere ◽  
2019 ◽  
Vol 4 (2) ◽  
Author(s):  
Anna M. Seekatz ◽  
Matthew K. Schnizlein ◽  
Mark J. Koenigsknecht ◽  
Jason R. Baker ◽  
William L. Hasler ◽  
...  
Keyword(s):  
Gastrointestinal Tract ◽  
Upper Gastrointestinal Tract ◽  
Rrna Gene ◽  
Gi Tract ◽  
Microbial Composition ◽  
Content Type ◽  
Healthy Humans ◽  
Health And Disease ◽  
Upper Gastrointestinal ◽  
Over Time

ABSTRACTAlthough the microbiota in the proximal gastrointestinal (GI) tract have been implicated in health and disease, much about these microbes remains understudied compared to those in the distal GI tract. This study characterized the microbiota across multiple proximal GI sites over time in healthy individuals. As part of a study of the pharmacokinetics of oral mesalamine administration, healthy, fasted volunteers (n = 8; 10 observation periods total) were orally intubated with a four-lumen catheter with multiple aspiration ports. Samples were taken from stomach, duodenal, and multiple jejunal sites, sampling hourly (≤7 h) to measure mesalamine (administered att = 0), pH, and 16S rRNA gene-based composition. We observed a predominance ofFirmicutesacross proximal GI sites, with significant variation compared to stool. The microbiota was more similar within individuals over time than between subjects, with the fecal microbiota being unique from that of the small intestine. The stomach and duodenal microbiota displayed highest intraindividual variability compared to jejunal sites, which were more stable across time. We observed significant correlations in the duodenal microbial composition with changes in pH; linear mixed models identified positive correlations with multipleStreptococcusoperational taxonomic units (OTUs) and negative correlations with multiplePrevotellaandPasteurellaceaeOTUs. Few OTUs correlated with mesalamine concentration. The stomach and duodenal microbiota exhibited greater compositional dynamics than the jejunum. Short-term fluctuations in the duodenal microbiota were correlated with pH. Given the unique characteristics and dynamics of the proximal GI tract microbiota, it is important to consider these local environments in health and disease states.IMPORTANCEThe gut microbiota are linked to a variety of gastrointestinal diseases, including inflammatory bowel disease. Despite this importance, microbiota dynamics in the upper gastrointestinal tract are understudied. Our article seeks to understand what factors impact microbiota dynamics in the healthy human upper gut. We found that the upper gastrointestinal tract contains consistently prevalent bacterial OTUs that dominate the overall community. Microbiota variability is highest in the stomach and duodenum and correlates with pH.

scholarly journals Simulating the Impact of Climate Change on the Hydrological Regimes of a Sparsely Gauged Mountainous Basin, Northern Pakistan

Water ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 2141 ◽  
Author(s):  
Saddique ◽  
Usman ◽  
Bernhofer
Keyword(s):  
Climate Change ◽  
River Basin ◽  
Assessment Tool ◽  
High Elevation ◽  
Climate Simulation ◽  
Water Yield ◽  
Research Station ◽  
Impact Of Climate Change ◽  
Global Circulation Models ◽  
The Impact

Projected climate changes for the 21st century may cause great uncertainties on the hydrology of a river basin. This study explored the impacts of climate change on the water balance and hydrological regime of the Jhelum River Basin using the Soil and Water Assessment Tool (SWAT). Two downscaling methods (SDSM, Statistical Downscaling Model and LARS-WG, Long Ashton Research Station Weather Generator), three Global Circulation Models (GCMs), and two representative concentration pathways (RCP4.5 and RCP8.5) for three future periods (2030s, 2050s, and 2090s) were used to assess the climate change impacts on flow regimes. The results exhibited that both downscaling methods suggested an increase in annual streamflow over the river basin. There is generally an increasing trend of winter and autumn discharge, whereas it is complicated for summer and spring to conclude if the trend is increasing or decreasing depending on the downscaling methods. Therefore, the uncertainty associated with the downscaling of climate simulation needs to consider, for the best estimate, the impact of climate change, with its uncertainty, on a particular basin. The study also resulted that water yield and evapotranspiration in the eastern part of the basin (sub-basins at high elevation) would be most affected by climate change. The outcomes of this study would be useful for providing guidance in water management and planning for the river basin under climate change.

Response of ecosystem functions to climate change and implications for sustainable development on the Inner Mongolian Plateau

2018 ◽  
Vol 40 (2) ◽  
pp. 191 ◽  
Author(s):  
Guozheng Hu ◽  
Jocelyn Davies ◽  
Qingzhu Gao ◽  
Cunzhu Liang
Keyword(s):  
Climate Change ◽  
Sustainable Development ◽  
Ecosystem Services ◽  
Future Climate ◽  
Ecosystem Functions ◽  
Carbon Exchange ◽  
Mongolian Plateau ◽  
Recent Climate Change ◽  
Recent Climate ◽  
The Impact

The responses of ecosystem functions in Inner Mongolian grasslands to climate change have implications for ecosystem services and sustainable development. Research published in two previous Special Issues of The Rangeland Journal shows that recent climate change added to overgrazing and other factors caused increased degradation of Inner Mongolian rangelands whereas on the Qinghai-Tibetan Plateau, climate change tended to ameliorate the impacts of overgrazing. Recent climate change on the Mongolian Plateau involved warming with increasingly variable annual precipitation and decreased summer rainfall. Future climate projections are different, involving modest increases in precipitation and further climate warming. Research published in the current Special Issue shows that precipitation is the climate factor that has the most substantial impact on ecosystem functions in this region and is positively correlated with plant species diversity, ecosystem carbon exchange and Normalised Difference Vegetation Index. Increased flows of provisioning and regulating ecosystem services are expected with future climate change indicating that its impacts will be positive in this region. However, spatial heterogeneity in the environments and climates of Inner Mongolia highlights the risk of over-generalising from local-scale studies and indicates the value of increased attention to meta-analysis and regional scale models. The enhanced flows of ecosystem services from climate change may support sustainable development by promoting recovery of degraded grasslands with flow-on benefits for livelihoods and the regional economy. However, realising these potential benefits will depend on sound landscape management and addressing the risk of herders increasing livestock numbers to take advantage of the extra forage available. Investment in education is important to improve local capacity to adapt rangeland management to climate change, as are policies and strategies that integrate social, economic and ecological considerations and are tailored to specific regions. Gaps in understanding that could be addressed through further research on ecosystem functions include; belowground carbon exchange processes; the impact of increased variability in precipitation; and the impact of different management practices under changed climates.

scholarly journals The urinary microbiota composition remains stable over time and under various storage conditions

2019 ◽  
Author(s):  
Caspar Bundgaard-Nielsen ◽  
Nadia Ammitzbøll ◽  
Yusuf Abdi Isse ◽  
Abdisalam Muqtar ◽  
Ann-Maria Jensen ◽  
...  
Keyword(s):  
Urinary Tract ◽  
Study Design ◽  
Storage Conditions ◽  
Rrna Gene ◽  
Microbiota Composition ◽  
Microbial Composition ◽  
Male Adult ◽  
Bacterial Composition ◽  
Urinary Microbiota ◽  
Over Time

AbstractBackgroundNew sensitive techniques have revealed a large population of bacteria in the human urinary tract, challenging the perception of the urine of healthy humans being sterile. While the role of this urinary microbiota is unknown, dysbiosis has been linked to disorders like urgency urinary incontinence and interstitial cystitis. When comparing studies it is crucial to account for possible confounders introduced due to methodological differences. Here we investigated whether storage condition or time of collection, had any impact on the urinary microbial composition.ResultsFor comparison of different storage conditions, urine was collected from five healthy adult female donors, and analyzed by 16S rRNA gene sequencing. Using the same methods, the daily or day-to-day variation in urinary microbiota was investigated in nineteen healthy donors, including four women, five men, five girls, and five boys. With the exception of two male adult donors, none of the tested conditions gave rise to significant differences in alpha and beta diversities between individuals. Conclusion: The composition of the urinary microbiota was found to be highly resilient to changes introduced by storage temperature and duration. In addition, we did not observe any intrapersonal daily or day-to-day variations in microbiota composition in women, girls or boys.Together our study supports flexibility in study design, when conducting urinary microbiota studies.Author summaryThe discovery of bacteria native to the urinary tract in healthy people, a location previously believed to be sterile, has prompted research into the clinical potential of these bacteria. However, methodological weaknesses can significantly influence such studies, and thus development of robust techniques for investigating these bacteria are needed. In the present study, we investigated whether differences in storage following collection, could affect the bacterial composition of urine samples. Next, we investigated if this composition exhibited daily or day-to-day variations.Firstly, we found, that the bacterial composition of urine could be maintained by storage at −80 °C, −20 °C, or refrigerated at 4 °C. Secondly, the bacterial composition of urine remained stable over time. Overall, the results of this study provide information important to study design in future investigations into the clinical implications of urinary bacteria.

scholarly journals Gut Microbiota Composition Changes in Constipated Women of Reproductive Age

2021 ◽  
Vol 10 ◽  
Author(s):  
Hongxia Li ◽  
Jianwei Chen ◽  
Xiaojing Ren ◽  
Chuanli Yang ◽  
Shuai Liu ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Chronic Constipation ◽  
Reproductive Age ◽  
Rrna Gene ◽  
Pathophysiological Mechanism ◽  
Healthy Controls ◽  
Women Of Reproductive Age ◽  
Microbial Composition ◽  
Hormone Levels ◽  
The Impact

BackgroundChronic constipation is one of the most prevalent functional gastrointestinal disorders, yet its etiology is multifactorial, and the pathophysiological mechanism is still unclear. Previous studies have shown that the gut microbiota of constipated patients differs from healthy controls; however, many discrepancies exist in the findings, and no clear link has been confirmed between chronic constipation and changes in the gut microbiota. Growing evidence indicates that age, gender, and hormone levels can affect the composition of gut microbiota. The aim of this study is to examine the overall changes in gut microbiota within a specific sub-population of patients, namely, constipated women of reproductive age.MethodsWe carried out a cross-sectional study comparing the fecal microbial composition of 30 healthy women and 29 constipated women using 16S rRNA gene sequencing. Only women of reproductive age were recruited to reduce the effects of age, gender, and hormone levels on the microbiome, and to prevent conflating the impact of these factors with the effects of constipation.ResultsThere were obvious differences in the gut microbiota in constipated women of reproductive age compared with the healthy controls, manifesting mainly as a significant increase in the abundance of Bacteroides (p < 0.05) and a significant decrease in the abundance of Proteobacteria (p < 0.01). The overall composition of the gut microbiota in each group was different, which was reflected in the ratios of Firmicutes to Bacteroidetes (F/B), which was 1.52 in the constipated group vs. 2.21 in the healthy group. Additionally, there was a significant decrease in butyrate-producing bacteria, like Roseburia and Fusicatenibacter (p < 0.01).ConclusionThe overall composition of the gut microbiota changed in constipated women of reproductive age, characterized by a loss in Proteobacteria and an increase in Bacteroidetes. Furthermore, the abundance of some butyrate-producing bacteria also reduced. These changes may reflect the unique interactions between host and some bacteria, or some bacterial metabolic products, which may be important targets for future studies to explore the pathogenesis of constipation.

scholarly journals Legionella pneumophila infection and antibiotic treatment engenders a highly disturbed pulmonary microbiome with decreased microbial diversity

2019 ◽  
Author(s):  
Ana Elena Pérez-Cobas ◽  
Christophe Ginevra ◽  
Christophe Rusniok ◽  
Sophie Jarraud ◽  
Carmen Buchrieser
Keyword(s):  
Antibiotic Treatment ◽  
Legionella Pneumophila ◽  
Severe Pneumonia ◽  
Resistant Bacteria ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Bacterial Composition ◽  
Lung Microbiome ◽  
The Impact ◽  
Healthy Lung

ABSTRACTBackgroundLung microbiome analyses have shown that the healthy lung is not sterile but it is colonized like other body sites by bacteria, fungi and viruses. However, little is known about the microbial composition of the lung microbiome during infectious diseases such as pneumonia and how it evolves during antibiotic therapy. To better understand the impact of the composition of the pulmonary microbiome on severity and outcome of pneumonia we analysed the composition and evolution of the human lung microbiome during pneumonia caused by the bacterium Legionella pneumophila.ResultsWe collected 10 bronchoalveolar lavage (BAL) samples from three patients during long-term hospitalisation due to severe pneumonia and performed a longitudinal in-depth study of the composition of their lung microbiome by high-throughput Illumina sequencing of the 16S rRNA gene (bacteria and archaea), ITS region (fungi) and 18S rRNA gene (eukaryotes). We found that the composition of the bacterial lung microbiome during pneumonia is hugely disturbed containing a very high percentage of the pathogen, a very low bacterial diversity, and an increased presence of opportunistic microorganisms such as species belonging to Staphylococcaceae and Streptococcaceae. The microbiome of antibiotic treated patients cured from pneumonia represented a different perturbation state with a higher abundance of resistant bacteria (mainly Firmicutes) and a significantly different bacterial composition as that found in healthy individuals. In contrast, the mycobiome remains more stable during pneumonia and antimicrobial therapy. Interestingly we identified possible cooperation within and between both communities. Furthermore, archaea (Methanobrevibacter) and protozoa (Acanthamoeba and Trichomonas) were detected.ConclusionsBacterial pneumonia leads to a collapse of the healthy microbiome and a strongly disturbed bacterial composition of the pulmonary microbiome that is dominated by the pathogen. Antibiotic treatment allows some bacteria to regrow or recolonize the lungs but the restoration of a healthy lung microbiome composition is only regained a certain time after the antibiotic treatment. Archaea and protozoa should also be considered, as they might be important but yet overseen members of the lung microbiome. Interactions between the micro- and the mycobiome might play a role in the restoration of the microbiome and the clinical evolution of the disease.

scholarly journals Influence of hydropower stations on the water microbiota in the downstream of Jinsha River, China

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9500
Author(s):  
Xiaojuan Chen ◽  
Da He ◽  
Lianfeng Zhou ◽  
Yankun Cao ◽  
Zhanjing Li
Keyword(s):  
Algal Blooms ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequencing ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Jinsha River ◽  
Kegg Pathways ◽  
Significant Difference ◽  
The Impact ◽  
Hydropower Stations

Construction of hydropower stations has been an important approach to meet China’s increasing power demand, but the impact of construction of hydropower stations on river microbiota is not fully understood. To evaluate this, the microbial composition from 18 sampling sites in the downstream of Jinsha River of China, upstream and downstream of two completed and two under-construction hydropower stations, were analyzed using high-throughput 16S rRNA gene sequencing. Three independent samples from each site were analyzed. A total of 18,683 OTUs from 1,350 genera were identified at 97% sequence similarity. Our results showed that the completion of hydropower stations would significantly increase the relative abundances of Acidobacteria, Chlorobi, Chloroflexi, Cyanobacteria, Nitrospirae, and Planctomycetes, especially the relative abundance of Synechococcus dOTUs and thus increase the risk of algal blooms. PCA based on all KEGG pathways and the significantly different KEGG pathways showed the predicted metabolic characteristics of the water microbiota by PICRUSt in the activated hydropower station group were significant difference to the other groups. Results from canonical correspondence analysis showed that water temperature and dissolved oxygen had significant effects on microbiota composition. These results are important for assessing the impact of hydropower stations on river microbiota and their potential environmental risks.

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