Journal articles on the topic 'Microbial community of soil, surface and groundwater'
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Turky, Azza Sh. "Microbial community in rural shallow groundwater affected by surface contaminated soil." International Journal of Academic Research 4, no. 4 (August 7, 2012): 188–97. http://dx.doi.org/10.7813/2075-4124.2012/4-4/a.26.
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Vargha, M., Z. Somlai, Z. Takáts, and K. Márialigeti. "Microbiological impact of atrazine pollution in river sediment and soil." Acta Agronomica Hungarica 52, no. 3 (November 1, 2004): 297–308. http://dx.doi.org/10.1556/aagr.52.2004.3.11.
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Atrazine is a frequently detected pollutant in agricultural soils, groundwater and surface waters. Microbial degradation was confirmed in soils, and recently several atrazine-degrading bacteria have been isolated. Degradation in aquifers, however, is not well understood, and to date, atrazine degraders have not been isolated from water. In the present study, the impact of atrazine was assessed in agricultural soil and river sediment and the composition of the atrazine-degrading bacterial community in the soil and sediment was compared. Atrazine pollution increased the number and diversity of the endogenous atrazine degraders in both environments. Proteobacteria were predominant atrazine degraders in soils, whereas the community of atrazine-degrading bacteria in sediment consisted mostly of coryneforms.
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Aislabie, J., J. Ryburn, and A. Sarmah. "Culturable microbes in shallow groundwater underlying ornithogenic soil of Cape Hallett, AntarcticaThis article is one of a selection of papers in the Special Issue on Polar and Alpine Microbiology." Canadian Journal of Microbiology 55, no. 1 (January 2009): 12–20. http://dx.doi.org/10.1139/w08-118.
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The objective of this study was to investigate the culturable psychrotolerant microbial community in groundwater from Seabee Hook, Antarctica. Shallow groundwater can be present in coastal regions at higher latitudes during the Antarctic summer. Perched groundwater atop ice-cemented permafrost occurs on Seabee Hook, Cape Hallett, at depths from 5 to 80 cm below the soil surface. Compared with terrestrial water from other sites in Antarctica, the groundwater was high in salt and nutrients, reflecting proximity to the sea and ornithogenic soil. Microbial communities in groundwater samples from Seabee Hook exhibited aerobic metabolism of14C-acetate at 5 °C. Numbers of culturable aerobic heterotrophs in the samples ranged from <10 to ca. 1 × 106 colony-forming units·mL–1, and similar numbers of microaerophiles and nitrate reducers were detected. In contrast, numbers of nitrifiers, sulfate reducers, and iron reducers were up to 1000-fold lower. All cultures were incubated at 5 °C. Aerobic heterotrophic bacteria isolated from the groundwater were assigned to Actinobacteria, Proteobacteria, or Bacteroidetes. The isolates were most similar to cultured bacteria from Antarctic soil or sediment and were cold, salt, and alkaline pH tolerant, indicating they are adapted to in situ conditions.
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Wakelin, Steven A., Paul N. Nelson, John D. Armour, Velupillai Rasiah, and Matthew J. Colloff. "Bacterial community structure and denitrifier (nir-gene) abundance in soil water and groundwater beneath agricultural land in tropical North Queensland, Australia." Soil Research 49, no. 1 (2011): 65. http://dx.doi.org/10.1071/sr10055.
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We explored the microbial ecology of water draining through the soil (lysimeter samples) and in the shallow aquifers (bore samples) underlying sugarcane and banana fields near the Great Barrier Reef (GBR), Australia. Lysimeter and bore water samples were collected and analysed chemically and with DNA fingerprinting methods (PCR-DGGE and clone library sequencing) to characterise the structure of the bacterial community. Bacterial communities in soil water and bore water were distinct (P < 0.05), and a primary factor linked with bacterial community structure was water pH (P < 0.05), particularly in water sampled from lysimeters. Irrespective of treatment, >80% of all rRNA gene sequences originated from proteobacteria. However, groundwater communities differed from those in soil water by greater occurrence of Neisseriales and Comamonadaceae (P < 0.01). qPCR was used to measure copy numbers of the nirK and nirS genes encoding NO-forming nitrite reductases. Copy numbers of both genes were greater in soil water samples than groundwater (P = 0.05), with the difference in nirK being greater under sugarcane than banana. These differences in nirK-gene abundance show that there is greater potential for denitrification in soil water under sugarcane, leading to low concentrations of nitrate in the underlying groundwater. This knowledge can be used towards development of soil and land-use management practices promoting bacterial denitrification in groundwater to lessen the undesirable ecological consequences where groundwater discharges lower in the GBR catchment zones.
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Moore-Kucera, Jennifer, Anita Nina Azarenko, Lisa Brutcher, Annie Chozinski, David D. Myrold, and Russell Ingham. "In Search of Key Soil Functions to Assess Soil Community Management for Sustainable Sweet Cherry Orchards." HortScience 43, no. 1 (February 2008): 38–44. http://dx.doi.org/10.21273/hortsci.43.1.38.
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Organic growers are required to maintain or improve soil chemical, biological, and physical properties and thus need to integrate biological processes into fertility management. However, few guidelines exist for satisfying tree nutrient demands ecologically. Sound nitrogen (N) management is a key component for overall orchard productivity whereas poor N management may result in multiple environmental impacts, including runoff to surface or leaching to groundwater sources. Many growers substitute synthetic inputs with rapid-release, approved N fertilizers that have little effect on long-term soil health and fertility. The authors seek an alternative approach for synchronizing nutrient availability with tree demand that relies on managing soil biological communities to attain their maximum potential functionality and thus meet tree nutrient demand. This paper outlines a new conceptual framework with which to evaluate a variety of soil functions that are quantified using biological, microbial, and biochemical properties in relation to overall orchard performance. By combining information gathered from soil faunal indices (nematode community structure and diversity analyses) with data obtained by biochemical and microbial analyses of the soil samples, a new, in-depth view of soil communities and their response to management practices will be obtained. As a result, a better understanding of the effects of differing management practices on soil fertility and community structure will be gained. This approach is currently being investigated by our group in organic and integrative sweet cherry orchards. Our goal is to determine which soil parameters may be used to help orchardists optimize soil health while maintaining orchard productivity. Furthermore, we wish to validate a number of assumptions that are commonly made regarding each soil parameter tested across multiple management, soil, and climate types.
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Mubeen, Bismillah, Ammarah Hasnain, Jie Wang, Hanxian Zheng, Syed Atif Hasan Naqvi, Ram Prasad, Ateeq ur Rehman, et al. "Current Progress and Open Challenges for Combined Toxic Effects of Manufactured Nano-Sized Objects (MNO’s) on Soil Biota and Microbial Community." Coatings 13, no. 1 (January 16, 2023): 212. http://dx.doi.org/10.3390/coatings13010212.
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Soil is a porous matrix containing organic matter and minerals as well as living organisms that vary physically, geographically, and temporally. Plants choose a particular microbiome from a pool of soil microorganisms which helps them grow and stay healthy. Many ecosystem functions in agrosystems are provided by soil microbes just like the ecosystem of soil, the completion of cyclic activity of vital nutrients like C, N, S, and P is carried out by soil microorganisms. Soil microorganisms affect carbon nanotubes (CNTs), nanoparticles (NPs), and a nanopesticide; these are called manufactured nano-objects (MNOs), that are added to the environment intentionally or reach the soil in the form of contaminants of nanomaterials. It is critical to assess the influence of MNOs on important plant-microbe symbiosis including mycorrhiza, which are critical for the health, function, and sustainability of both natural and agricultural ecosystems. Toxic compounds are released into rural and urban ecosystems as a result of anthropogenic contamination from industrial processes, agricultural practices, and consumer products. Once discharged, these pollutants travel through the atmosphere and water, settling in matrices like sediments and groundwater, potentially rendering broad areas uninhabitable. With the rapid growth of nanotechnology, the application of manufactured nano-objects in the form of nano-agrochemicals has expanded for their greater potential or their appearance in products of users, raising worries about possible eco-toxicological impacts. MNOs are added throughout the life cycle and are accumulated not only in the soils but also in other components of the environment causing mostly negative impacts on soil biota and processes. MNOs interfere with soil physicochemical qualities as well as microbial metabolic activity in rhizospheric soils. This review examines the harmful effect of MNOs on soil, as well as the pathways used by microbes to deal with MNOs and the fate and behavior of NPs inside the soils.
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Schütz, Kirsten, Ellen Kandeler, Peter Nagel, Stefan Scheu, and Liliane Ruess. "Functional microbial community response to nutrient pulses by artificial groundwater recharge practice in surface soils and subsoils." FEMS Microbiology Ecology 72, no. 3 (February 20, 2010): 445–55. http://dx.doi.org/10.1111/j.1574-6941.2010.00855.x.
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Sonthiphand, Prinpida, Supeerapat Kraidech, Saowarod Polart, Srilert Chotpantarat, Kanthida Kusonmano, Pichahpuk Uthaipaisanwong, Chalida Rangsiwutisak, and Ekawan Luepromchai. "Arsenic speciation, the abundance of arsenite-oxidizing bacteria and microbial community structures in groundwater, surface water, and soil from a gold mine." Journal of Environmental Science and Health, Part A 56, no. 7 (May 26, 2021): 769–85. http://dx.doi.org/10.1080/10934529.2021.1927421.
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Herrmann, Martina, Anna Rusznyák, Denise M. Akob, Isabel Schulze, Sebastian Opitz, Kai Uwe Totsche, and Kirsten Küsel. "Large Fractions of CO2-Fixing Microorganisms in Pristine Limestone Aquifers Appear To Be Involved in the Oxidation of Reduced Sulfur and Nitrogen Compounds." Applied and Environmental Microbiology 81, no. 7 (January 23, 2015): 2384–94. http://dx.doi.org/10.1128/aem.03269-14.
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ABSTRACTThe traditional view of the dependency of subsurface environments on surface-derived allochthonous carbon inputs is challenged by increasing evidence for the role of lithoautotrophy in aquifer carbon flow. We linked information on autotrophy (Calvin-Benson-Bassham cycle) with that from total microbial community analysis in groundwater at two superimposed—upper and lower—limestone groundwater reservoirs (aquifers). Quantitative PCR revealed that up to 17% of the microbial population had the genetic potential to fix CO2via the Calvin cycle, with abundances ofcbbMandcbbLgenes, encoding RubisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) forms I and II, ranging from 1.14 × 103to 6 × 106genes liter−1over a 2-year period. The structure of the active microbial communities based on 16S rRNA transcripts differed between the two aquifers, with a larger fraction of heterotrophic, facultative anaerobic, soil-related groups in the oxygen-deficient upper aquifer. Most identified CO2-assimilating phylogenetic groups appeared to be involved in the oxidation of sulfur or nitrogen compounds and harbored both RubisCO forms I and II, allowing efficient CO2fixation in environments with strong oxygen and CO2fluctuations. The generaSulfuricellaandNitrosomonaswere represented by read fractions of up to 78 and 33%, respectively, within thecbbMandcbbLtranscript pool and accounted for 5.6 and 3.8% of 16S rRNA sequence reads, respectively, in the lower aquifer. Our results indicate that a large fraction of bacteria in pristine limestone aquifers has the genetic potential for autotrophic CO2fixation, with energy most likely provided by the oxidation of reduced sulfur and nitrogen compounds.
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Balcom, Ian N., Heather Driscoll, James Vincent, and Meagan Leduc. "Metagenomic analysis of an ecological wastewater treatment plant’s microbial communities and their potential to metabolize pharmaceuticals." F1000Research 5 (July 28, 2016): 1881. http://dx.doi.org/10.12688/f1000research.9157.1.
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Pharmaceuticals and other micropollutants have been detected in drinking water, groundwater, surface water, and soil around the world. Even in locations where wastewater treatment is required, they can be found in drinking water wells, municipal water supplies, and agricultural soils. It is clear conventional wastewater treatment technologies are not meeting the challenge of the mounting pressures on global freshwater supplies. Cost-effective ecological wastewater treatment technologies have been developed in response. To determine whether the removal of micropollutants in ecological wastewater treatment plants (WWTPs) is promoted by the plant-microbe interactions, as has been reported for other recalcitrant xenobiotics, biofilm microbial communities growing on the surfaces of plant roots were profiled by whole metagenome sequencing and compared to the microbial communities residing in the wastewater. In this study, the concentrations of pharmaceuticals and personal care products (PPCPs) were quantified in each treatment tank of the ecological WWTP treating human wastewater at a highway rest stop and visitor center in Vermont. The concentrations of detected PPCPs were substantially greater than values reported for conventional WWTPs likely due to onsite recirculation of wastewater. The greatest reductions in PPCPs concentrations were observed in the anoxic treatment tank where Bacilli dominated the biofilm community. Benzoate degradation was the most abundant xenobiotic metabolic category identified throughout the system. Collectively, the microbial communities residing in the wastewater were taxonomically and metabolically more diverse than the immersed plant root biofilm. However, greater heterogeneity and higher relative abundances of xenobiotic metabolism genes was observed for the root biofilm.
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Bolan, N. S., and V. P. Duraisamy. "Role of inorganic and organic soil amendments on immobilisation and phytoavailability of heavy metals: a review involving specific case studies." Soil Research 41, no. 3 (2003): 533. http://dx.doi.org/10.1071/sr02122.
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Soil is not only considered as a 'source' of nutrients for plant growth, but also as a 'sink' for the removal of contaminants from industrial and agricultural waste materials. The origin of heavy metal contamination of soils may be anthropogenic as well as geogenic. With greater public awareness of the implications of contaminated soils on human and animal health, there has been increasing interest amongst the scientific community in developing cost-effective and community-acceptable remediation technologies for contaminated sites. Unlike organic contaminants, most metals do not undergo microbial or chemical degradation, thereby resulting in their accumulation in soils. The mobilisation of metals in soils for plant uptake and leaching to groundwater can, however, be minimised through chemical and biological immobilisation. Recently there has been increasing interest in the immobilisation of metals using a range of inorganic compounds, such as lime and phosphate (P) compounds, and organic compounds, such as 'exceptional quality' biosolids. In this review paper, the results from selected New Zealand studies on the potential value of a range of soil amendments (phosphate compounds, liming materials, and biosolids) in the immobilisation of cadmium (Cd), chromium (Cr), and copper (Cu) is discussed in relation to remediation of contaminated soils. These case studies have indicated that lime is effective in reducing the phytoavailability of Cd and Cr(III), phosphate compounds are effective for Cd, and organic amendments are effective for Cu and Cr(VI). The mechanisms proposed for the immobilisation and consequent reduction in the phytoavailability of metals by the soil amendments include: enhanced metal adsorption through increased surface charge (e.g. phosphate-induced metal adsorption), increased formation of organic and inorganic metal complexes (e.g. cadmium-phosphate complex and copper-organic matter complex), precipitation of metals (e.g. chromic hydroxide), and reduction of metals from higher valency mobile form to lower valency immobile form [e.g. Cr(VI) to Cr(III)]. These case studies indicated that since bioavailability is the key factor for remediation technologies, chemical or biological immobilisation of metals may be a preferred option.
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Morse, Kendall V., Dylan R. Richardson, Teresa L. Brown, Robert D. Vangundy, and Aubrey Bruce Cahoon. "Longitudinal metabarcode analysis of karst bacterioplankton microbiomes provide evidence of epikarst to cave transport and community succession." PeerJ 9 (March 8, 2021): e10757. http://dx.doi.org/10.7717/peerj.10757.
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Caves are often assumed to be static environments separated from weather changes experienced on the surface. The high humidity and stability of these subterranean environments make them attractive to many different organisms including microbes such as bacteria and protists. Cave waters generally originate from the surface, may be filtered by overlying soils, can accumulate in interstitial epikarst zones underground, and emerge in caves as streams, pools and droplets on speleothems. Water movement is the primary architect of karst caves, and depending on the hydrologic connectivity between surface and subsurface, is the most likely medium for the introduction of microbes to caves. Recently published metabarcoding surveys of karst cave soils and speleothems have suggested that the vast majority of bacteria residing in these habitats do not occur on the surface, calling into question the role of microbial transport by surface waters. The purpose of this study was to use metabarcoding to monitor the aquatic prokaryotic microbiome of a cave for 1 year, conduct longitudinal analyses of the cave’s aquatic bacterioplankton, and compare it to nearby surface water. Water samples were collected from two locations inside Panel Cave in Natural Tunnel State Park in Duffield, VA and two locations outside of the cave. Of the two cave locations, one was fed by groundwater and drip water and the other by infiltrating surface water. A total of 1,854 distinct prokaryotic ASVs were detected from cave samples and 245 (13.1%) were not found in surface samples. PCo analysis demonstrated a marginal delineation between two cave sample sites and between cave and surface microbiomes suggesting the aquatic bacterioplankton in a karst cave is much more similar to surface microbes than reported from speleothems and soils. Most surprisingly, there was a cave microbe population and diversity bloom in the fall months whereas biodiversity remained relatively steady on the surface. The cave microbiome was more similar to the surface before the bloom than during and afterwards. This event demonstrates that large influxes of bacteria and particulate organic matter can enter the cave from either the surface or interstitial zones and the divergence of the cave microbiome from the surface demonstrates movement of microbes from the epikarst zones into the cave.
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Barba, Carme, Albert Folch, Núria Gaju, Xavier Sanchez-Vila, Marc Carrasquilla, Alba Grau-Martínez, and Maira Martínez-Alonso. "Microbial community changes induced by Managed Aquifer Recharge activities: linking hydrogeological and biological processes." Hydrology and Earth System Sciences 23, no. 1 (January 11, 2019): 139–54. http://dx.doi.org/10.5194/hess-23-139-2019.
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Abstract. Managed Aquifer Recharge (MAR) is a technique used worldwide to increase the availability of water resources. We study how MAR modifies microbial ecosystems and its implications for enhancing biodegradation processes to eventually improve groundwater quality. We compare soil and groundwater samples taken from a MAR facility located in NE Spain during recharge (with the facility operating continuously for several months) and after 4 months of no recharge. The study demonstrates a strong correlation between soil and water microbial prints with respect to sampling location along the mapped infiltration path. In particular, managed recharge practices disrupt groundwater ecosystems by modifying diversity indices and the composition of microbial communities, indicating that infiltration favors the growth of certain populations. Analysis of the genetic profiles showed the presence of nine different bacterial phyla in the facility, revealing high biological diversity at the highest taxonomic range. In fact, the microbial population patterns under recharge conditions agree with the intermediate disturbance hypothesis (IDH). Moreover, DNA sequence analysis of excised denaturing gradient gel electrophoresis (DGGE) band patterns revealed the existence of indicator species linked to MAR, most notably Dehalogenimonas sp., Nitrospira sp. and Vogesella sp.. Our real facility multidisciplinary study (hydrological, geochemical and microbial), involving soil and groundwater samples, indicates that MAR is a naturally based, passive and efficient technique with broad implications for the biodegradation of pollutants dissolved in water.
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Villeneuve, Karine, Michel Violette, and Cassandre Sara Lazar. "From Recharge, to Groundwater, to Discharge Areas in Aquifer Systems in Quebec (Canada): Shaping of Microbial Diversity and Community Structure by Environmental Factors." Genes 14, no. 1 (December 20, 2022): 1. http://dx.doi.org/10.3390/genes14010001.
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Groundwater recharge and discharge rates and zones are important hydrogeological characteristics of aquifer systems, yet their impact on the formation of both subterranean and surface microbiomes remains largely unknown. In this study, we used 16S rRNA gene sequencing to characterize and compare the microbial community of seven different aquifers, including the recharge and discharge areas of each system. The connectivity between subsurface and surface microbiomes was evaluated at each site, and the temporal succession of groundwater microbial communities was further assessed at one of the sites. Bacterial and archaeal community composition varied between the different sites, reflecting different geological characteristics, with communities from unconsolidated aquifers being distinct from those of consolidated aquifers. Our results also revealed very little to no contribution of surface recharge microbial communities to groundwater communities as well as little to no contribution of groundwater microbial communities to surface discharge communities. Temporal succession suggests seasonal shifts in composition for both bacterial and archaeal communities. This study demonstrates the highly diverse communities of prokaryotes living in aquifer systems, including zones of groundwater recharge and discharge, and highlights the need for further temporal studies with higher resolution to better understand the connectivity between surface and subsurface microbiomes.
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Ramachandra, T. V. "Innovative ecological approaches to ensure clean and adequate water for all." Journal of Environmental Biology 43, no. 03 (May 2, 2022): i—ii. http://dx.doi.org/10.22438/jeb/43/3/editorial.
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The Western Ghats, a range of ancient hills extends between 8° N and 21° N latitude, and 73° E and 77° E longitude(from the tip of peninsular India at Kanyakumari to Gujarat). The Western Ghats runs parallel to the west coast of India, covering approximately 160,000 sq. km, which constitutes less than 5% of India's geographical extent. Numerous streams originate in the Western Ghats, which drain millions of hectares, ensuring water and food security for 245 million people and hence are aptly known as the water tower of peninsular India(Ramachandra and Bharath, 2019; Bharath et al., 2021). The region is endowed with diverse ecological regions depending on altitude, latitude, rainfall, and soil characteristics. The Western Ghats are among the eight hottest hotspots of biodiversity and 36 global biodiversity hotspots with exceptional endemic flora and fauna. Natural forests of Western Ghats have been providing various goods and services and are endowed with species of 4,600+ flowering plants (38% endemics), 330 butterflies (11% endemics), 156 reptiles (62% endemics), 508 birds (4% endemics), 120 mammals (12% endemics), 289 fishes (41% endemics) and 135 amphibians (75% endemics). The Western Ghats, gifted with enormous natural resource potential, and the mandate of sustainable development based on the foundation of prudent management of ecosystems, is yet a reality. Various unplanned developmental programs, which are proclaimed to be functioning on sustainability principles, have only been disrupting the complex web of life, impacting ecosystems, and causing a decline in overall productivity, including four major sectors: forestry, fisheries, agriculture, and water (Ramachandra and Bharath, 2019).The prevalence of barren hilltops, conversion of perennial streams to intermittent or seasonal streams, frequent floods and droughts, changes in water quality, soil erosion and sedimentation, the decline of endemic flora, and fauna, etc. highlights the consequences of unplanned developmental activities with a huge loss to the regional economy during the last century. The development goals need to be ecologically, economically, and socially sustainable, which can be achieved through the conservation and prudent management of ecosystems. Sustainability implies the equilibrium between society, ecosystem integrity, and sustenance of natural resources. Water sustenance in streams and rivers depends on the integrity of the catchment (watershed), as vegetation helps in retarding the velocity of water by allowing impoundment and recharging of groundwater through infiltration (Ramachandra et al., 2020). As water moves in the terrestrial ecosystem, part of it is percolated (recharging groundwater resources and contributing to sub-surface flow during post-monsoon seasons), while another fraction gets back to the atmosphere through evaporation and transpiration. Forests with native vegetation act as a sponge by retaining and regulating water transfer between land and the atmosphere. The mechanism by which vegetation controls flow regime is dependent on various bio-physiographic characteristics, namely, type of vegetation, species composition, maturity, density, root density and depth, hydro-climatic condition, etc. Roots of vegetation help (i) in binding soil, ii) improve soil structure by enhancing the stability of aggregates, which provide habitat for diverse microfauna and flora, leading to higher porosity of the soil, thereby creating the conduit for infiltration through the soil. An undisturbed native forest has a consistent hydrologic regime with sustained flows during lean seasons. Native species of vegetation with the assemblage of diverse native species help in recharging the groundwater, mitigating floods, and other hydro-ecological processes (Ramachandra et al., 2020; Bharath et al., 2021). Hence, it necessitates safeguarding and maintaining native forest patches and restoring existing degraded lands to sustain the hydrological regime, which caters to biotic (ecological and societal) demands. A comparative assessment of people's livelihood with soil water properties and water availability in sub-catchments of four major river basins in the Western Ghats reveals that streams in catchments with > 60% vegetation of native species are perennial with higher soil moisture (Ramachandra et al., 2020). The higher soil moisture due to water availability during all seasons facilitates farming of commercial crops with higher economic returns to the farmers, unlike the farmers who face water crises during the lean season. In contrast, streams are intermittent (6-8 months of water) in catchments dominated by monoculture plantations and seasonal (4 months, monsoon period) in catchments with vegetation cover lower than 30%. The study highlights the need to maintain ecosystem integrity to sustain water. Also, lower instances of COVID 19 in villages with native forests emphasize ecosystems' role in maintaining the health of biota. The need to maintain native vegetation in the catchment and its potential to support people's livelihood with water availability at local and regional levels is evident from the revenue of Rs. Rs.2,74,658 ha-1 yr-1 (in villages with perennial streams and farmers growing cash crops or three crops a year due to water availability), Rs. 1,50,679 ha-1 yr-1 (in villages with intermittent streams) and Rs. 80000 ha-1 yr-1 (in villages with seasonal streams). Also, the crop yield (at least 1.5 to 1.8 times) is higher in agriculture fields due to efficient pollination with the prevalence of diverse pollinators in the vicinity of native forests. The study emphasizes the need for maintaining the natural flow regime and prudent management of watershed to i) sustain higher faunal diversity, ii) maintain the health of water body, and iii) sustain people's livelihood with higher revenues. Hence, the premium should be on conserving the forests with native species to sustain water and biotic diversity in the water bodies, vital for food security. There still exists a chance to restore the lost natural ecosystems through appropriate ecological restoration approaches, with location-specific conservation and management practices to ensure adequate and clean water for all. GDP (Gross Domestic Product), a measure of the current economic well-being of a population, based on the market exchange of material well-being, will indicate resource depletion/degradation only through a positive gain in the economy and will not represent the decline in these assets (wealth) at all. Thus, the existing GDP growth percentages used as yardsticks to measure the development and well-being of citizens in decision-making processes are substantially misleading, yet they are being used. The traditional national accounts need to include resource depletion or degradation due to developmental activities and climate change. The country should move toward adopting Green GDP by accounting for the environmental consequences of the growth in the conventional GDP, which entails monetizing the services provided by ecosystems, the degradation cost of ecosystems, and accounts for costs caused by climate change. The forest ecosystems are under severe threat due to anthropogenic pressures, which are mostly related to the GDP.The appraisal of forest ecosystem services and biodiversity can help clarify trade-offs among conflicting environmental, social, and economic goals in the development and implementation of policies and to improve the management in order biodiversity.Natural capital accounting and valuation of ecosystem services reveal that forest ecosystems provide (i) provisioning services (timber, fuelwood, food, NTFP, medicines, genetic materials) of Rs 2,19,494 ha-1 yr-1, (ii) regulating services (global climate regulation - carbon sequestration, soil conservation, and soil fertility, water regulation and groundwater recharge, water purification, pollination, waste treatment, air filtration, local climate regulation) of Rs 3,31,216 ha-1 yr-1 and (iii) cultural services (aesthetic, spiritual, tourism and recreation, education and scientific research) of Rs.1,04,561 ha-1 yr-1. Total ecosystem supply value (TESV), an aggregation of provisioning, regulating, and cultural services, amounts to Rs. 6,56,172 ha-1 yr-1, and the Net Present Value (NPV) of one hectare of forests amounts to 16.88 million rupees ha-1. NPV helps in estimating ecological compensation while diverting forest lands for other purposes. The recovery of an ecosystem with respect to its health, integrity, and sustainability is evident from an initiative of planting (500 saplings of 49 native species) in a degraded landscape (dominated by invasive species) of two hectares in the early 1990s at the Indian Institute of Science campus (Ramachandra et al., 2016),and the region has now transformed into a mini forest with numerous benefits such as improvements in groundwater at 3-6 m (compared to 30-40 m in 1990), moderated microclimate (with lower temperature) and numerous fauna (including four families of Slender Loris). While confirming the linkages of hydrology, ecology, and biodiversity, the experiment advocates the need for integrated watershed approaches based on sound ecological and engineering protocols to sustain water and ensure adequate water for all. A well-known and successful model of integrated wetlands ecosystem (Secondary treatment plant integrated with constructed wetlands and algae pond) at Jakkur Lake in Bangalore (Ramachandra et al., 2018) provides insights into the optimal treatment of wastewater and mitigation of pollution. Complete removal of nutrients and chemical contaminants happens when partially treated sewage (secondary treated) passes through constructed wetlands and algae pond (sedimentation pond), undergoes bio-physical and chemical processes. The water in the lake is almost potable with minimal nutrients and microbial counts. This model has been functioning successfully for the last ten years after interventions to rejuvenate the lake. This system is one of the self-sustainable ways of lake management while benefitting all stakeholders - washing, fishing, irrigation, and local people. Wells in the buffer zone (500 m), now have higher water levels and are without any nutrients (nitrate). Groundwater quality assessment in 25 wells in the same region during 2005 (before the rejuvenation of Jakkur Lake) had higher nitrate values. Adopting this model ensures optimal sewage treatment at decentralized levels, and letting treated water to the lake also provides nutrient-free and clean groundwater. The Jal Shakti ministry,the Government of India, through Jal Jeevan Mission, has embarked on the noble and novel mission of providing tap water supply to all rural households and public institutions in villages such as schools, health centers, panchayat buildings, etc. The success of this program depends on the availability of water. The imminent threat of acute water scarcity due to climate changes with global warming necessitates implementing integrated watershed development (planting of native species in the watershed of water bodies), rainwater harvesting (rooftop harvesting at individual household levels, and retaining rainwater in rejuvenated lakes, which also helps in recharge of groundwater) and reuse of wastewater through treatment at decentralized levels (a model similar to Jakkur lake at Bangalore). These prudent management initiatives at decentralized levels throughout the country aid in achieving the goals of providing clean and adequate water to the local community.
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DeAngelis, Kristen M., Cindy H. Wu, Harry R. Beller, Eoin L. Brodie, Romy Chakraborty, Todd Z. DeSantis, Julian L. Fortney, et al. "PCR Amplification-Independent Methods for Detection of Microbial Communities by the High-Density Microarray PhyloChip." Applied and Environmental Microbiology 77, no. 18 (July 15, 2011): 6313–22. http://dx.doi.org/10.1128/aem.05262-11.
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ABSTRACTEnvironmental microbial community analysis typically involves amplification by PCR, despite well-documented biases. We have developed two methods of PCR-independent microbial community analysis using the high-density microarray PhyloChip: direct hybridization of 16S rRNA (dirRNA) or rRNA converted to double-stranded cDNA (dscDNA). We compared dirRNA and dscDNA communities to PCR-amplified DNA communities using a mock community of eight taxa, as well as experiments derived from three environmental sample types: chromium-contaminated aquifer groundwater, tropical forest soil, and secondary sewage in seawater. Community profiles by both direct hybridization methods showed differences that were expected based on accompanying data but that were missing in PCR-amplified communities. Taxon richness decreased in RNA compared to that in DNA communities, suggesting a subset of 20% in soil and 60% in groundwater that is active; secondary sewage showed no difference between active and inactive populations. Direct hybridization of dscDNA and RNA is thus a viable alternative to PCR-amplified microbial community analysis, providing identification of the active populations within microbial communities that attenuate pollutants, drive global biogeochemical cycles, or proliferate disease states.
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Ryabova, A. S., L. Y. Kuzmina, and N. F. Galimzyanova. "MICROBIAL COMMUNITY OF THE ASKINSKAYA CAVE." ÈKOBIOTEH 4, no. 3 (2021): 186–94. http://dx.doi.org/10.31163/2618-964x-2021-4-3-186-194.
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The cave Askinskaya (Askynskaya, Ledyanaya) contains the largest perennial hydrogenic ice in the territory of the Southern Urals. It is shown that the soil and horizontal hydrogenic ice are the main reservoirs for storing microorganisms in the cave, and the microbial pool is replenished mainly due to recreational load, but natural ways – rain, melt water and air from the surface also make a certain contribution. From all the ecotopes of the cave (soil, water occurrences, rock surfaces and aerial environment), 72 species of microscopic fungi (D – 0.69), sterile forms and yeast were isolated. Yeast fungi and species of Geomyces pannorum (d – 0.83), Acremonium charticola, Cladosporium herbarum, Penicillium aurantiuogriseum were found in all ecological niches with a high frequency of abundance / occurrence. The greatest variety of microscopic fungi is observed in the air (57 species), most species are introduced from the surface, settle on walls, ice, soil and, due to low temperatures, retain their viability in the cavity for a long time.
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Pereira, Marlon Correa, Roisin O’Riordan, and Carly Stevens. "Urban soil microbial community and microbial-related carbon storage are severely limited by sealing." Journal of Soils and Sediments 21, no. 3 (January 29, 2021): 1455–65. http://dx.doi.org/10.1007/s11368-021-02881-7.
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Abstract Purpose Urbanisation causes changes in land use, from natural or rural to urban, leading to the sealing of soil and the replacement of vegetation by buildings, roads and pavements. The sealing process impacts soil properties and services and can lead to negative consequences for microbial attributes and processes in soil. At present, information about the microbial community following soil sealing is limited. As such, we investigated how changes in soil physical and chemical properties caused by sealing affect the soil microbial community and soil ecosystem services. Material and methods Soils were sampled beneath impervious pavements (sealed) and from adjacent pervious greenspace areas (unsealed). Soil properties (total C, total N, C:N ratio and water content) and microbial attributes (microbial biomass C, N-mineralisation and phospholipid fatty acids—PLFA) were measured and correlated. Results and discussion A reduction of total C, total N, and water content were observed in sealed soil, whilst the C:N ratio increased. Sealed soil also presented a reduction in microbial attributes, with low N-mineralisation revealing suppressed microbial activity. PLFA data presented positive correlations with total C, total N and water content, suggesting that the microbial community may be reduced in sealed soil as a response to soil properties. Furthermore, fungal:bacterial and gram-positive:gram-negative bacterial ratios were lower in sealed soil indicating degradation in C sequestration and a consequential effect on C storage. Conclusions Sealing causes notable changes in soil properties leading to subsequent impacts upon the microbial community and the reduction of microbial activity and soil C storage potential.
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Jacobsen, Carsten Suhr, Susanne Elmholt, Carsten Bagge Jensen, Pia Bach Jakobsen, and Mikkel Bender. "Steam treatment of contaminated groundwater aquifers – development of pathogenic micro-organisms in soil." Geological Survey of Denmark and Greenland (GEUS) Bulletin 7 (July 29, 2005): 37–40. http://dx.doi.org/10.34194/geusb.v7.4829.
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Steam treatment of contaminated soil and aquifer sediment is a promising method of cleaning soil. The treatment is based on steam injection into a water saturated porous aquifer (Gudbjerg et al. 2004), by which the heat transfers the contaminants into the vapour phase, allowing entrapment in an active carbon filter connected to a large vacuum suction device. The treatment is effective against several important groundwater contaminants, including pentachlorophenole and perchloroethylene, typically found in association with industrial processes or dry cleaning facilities. Furthermore, as an example of removal of non-aqueous phase liquids (NAPLs) large amounts of creosote have been recovered after steam injection in a deep aquifer (Kuhlmann 2002; Tse & Lo 2002). Steam treatment is dependent on the complete heating of the soil volume under treatment. The steam has a strongly adverse impact on trees and other plants with deep root systems within the soil, but no other visible effects have been reported. The aim of the activities undertaken during collaborative projects carried out by the Geological Survey of Denmark and Greenland (GEUS) and the Danish Institute of Agricultural Sciences (DJF) for the Danish Environmental Protection Agency and the local authorities in Copenhagen (Københavns Amt) was to establish to what extent the microbial community was affected by the steam treatment of the soil. A few results from the literature indicate that the microbial activity increases in steam treated soil (Richardson et al. 2002), probably due to microbial degradation of the soil contaminants in combination with microbial utilisation of heatkilled organisms. It is, however, not known whether this increased microbial activity is associated with the development of pathogenic micro-organisms; these are typically able to grow at higher temperatures than the general microbial community in soil.
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Li, Yaying, Juan Wang, Fuxiao Pan, Stephen James Chapman, and Huaiying Yao. "Soil nitrogen availability alters rhizodeposition carbon flux into the soil microbial community." Journal of Soils and Sediments 16, no. 5 (January 25, 2016): 1472–80. http://dx.doi.org/10.1007/s11368-015-1337-6.
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Cheng, C., D. Zhao, D. Lv, S. Li, and G. Du. "Comparative study on microbial community structure across orchard soil, cropland soil, and unused soil." Soil and Water Research 12, No. 4 (October 9, 2017): 237–45. http://dx.doi.org/10.17221/177/2016-swr.
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We examined the effects of three different soil conditions (orchard soil, cropland soil, unused soil) on the functional diversity of soil microbial communities. The results first showed that orchard and cropland land use significantly changed the distribution and diversity of soil microbes, particularly at surface soil layers. The richness index (S) and Shannon diversity index (H) of orchard soil microbes were significantly higher than the indices of the cropland and unused soil treatments in the 0–10 cm soil layer, while the S and H indices of cropland soil microbes were the highest in 10–20 cm soil layers. Additionally, the Simpson dominance index of cropland soil microbial communities was the highest across all soil layers. Next, we found that carbon source differences in soil layers under the three land use conditions can mainly be attributed to their carbohydrate and polymer composition, indicating that they are the primary cause of the functional differences in microbial communities under different land uses. In conclusion, orchard and cropland soil probably affected microbial distribution and functional diversity due to differences in vegetation cover, cultivation, and management measures.
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Wu, Tiehang, Ashley Gray, Gan Liu, Hilary Kaminski, Bolanle Osi Efa, and Doug P. Aubrey. "Groundwater Depth Overrides Tree-Species Effects on the Structure of Soil Microbial Communities Involved in Nitrogen Cycling in Plantation Forests." Forests 11, no. 3 (February 28, 2020): 275. http://dx.doi.org/10.3390/f11030275.
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Microbial communities found in soil ecosystems play important roles in decomposing organic materials and recycling nutrients. A clear understanding on how biotic and abiotic factors influence the microbial community and its functional role in ecosystems is fundamental to terrestrial biogeochemistry and plant production. The purpose of this study was to investigate microbial communities and functional genes involved in nitrogen cycling as a function of groundwater depth (deep and shallow), tree species (pine and eucalypt), and season (spring and fall). Soil fungal, bacterial, and archaeal communities were determined by length heterogeneity polymerase chain reaction (LH-PCR). Soil ammonia oxidation archaeal (AOA) amoA gene, ammonia oxidation bacterial (AOB) amoA gene, nitrite oxidoreductase nrxA gene, and denitrifying bacterial narG, nirK, nirS, and nosZ genes were further studied using PCR and denaturing gradient gel electrophoresis (DGGE). Soil fungal and bacterial communities remained similar between tree species and groundwater depths, respectively, regardless of season. Soil archaeal communities remained similar between tree species but differed between groundwater depths in the spring only. Archaeal amoA for nitrification and bacterial nirK and nosZ genes for denitrification were detected in DGGE, whereas bacterial amoA and nrxA for nitrification and bacterial narG and nirS genes for denitrification were undetectable. The detected nitrification and denitrification communities varied significantly with groundwater depth. There was no significant difference of nitrifying archaeal amoA or denitrifying nirK communities between different tree species regardless of season. The seasonal difference in microbial communities and functional genes involved in nitrogen cycling suggests microorganisms exhibit seasonal dynamics that likely impact relative rates of nitrification and denitrification.
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Mathew, Reji P., Yucheng Feng, Leonard Githinji, Ramble Ankumah, and Kipling S. Balkcom. "Impact of No-Tillage and Conventional Tillage Systems on Soil Microbial Communities." Applied and Environmental Soil Science 2012 (2012): 1–10. http://dx.doi.org/10.1155/2012/548620.
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Soil management practices influence soil physical and chemical characteristics and bring about changes in the soil microbial community structure and function. In this study, the effects of long-term conventional and no-tillage practices on microbial community structure, enzyme activities, and selected physicochemical properties were determined in a continuous corn system on a Decatur silt loam soil. The long-term no-tillage treatment resulted in higher soil carbon and nitrogen contents, viable microbial biomass, and phosphatase activities at the 0–5 cm depth than the conventional tillage treatment. Soil microbial community structure assessed using phospholipid fatty acid (PLFA) analysis and automated ribosomal intergenic spacer analysis (ARISA) varied by tillage practice and soil depth. The abundance of PLFAs indicative of fungi, bacteria, arbuscular mycorrhizal fungi, and actinobacteria was consistently higher in the no-till surface soil. Results of principal components analysis based on soil physicochemical and enzyme variables were in agreement with those based on PLFA and ARISA profiles. Soil organic carbon was positively correlated with most of the PLFA biomarkers. These results indicate that tillage practice and soil depth were two important factors affecting soil microbial community structure and activity, and conservation tillage practices improve both physicochemical and microbiological properties of soil.
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Zosso, Cyrill U., Nicholas O. E. Ofiti, Jennifer L. Soong, Emily F. Solly, Margaret S. Torn, Arnaud Huguet, Guido L. B. Wiesenberg, and Michael W. I. Schmidt. "Whole-soil warming decreases abundance and modifies the community structure of microorganisms in the subsoil but not in surface soil." SOIL 7, no. 2 (August 2, 2021): 477–94. http://dx.doi.org/10.5194/soil-7-477-2021.
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Abstract. The microbial community composition in subsoils remains understudied, and it is largely unknown whether subsoil microorganisms show a similar response to global warming as microorganisms at the soil surface do. Since microorganisms are the key drivers of soil organic carbon decomposition, this knowledge gap causes uncertainty in the predictions of future carbon cycling in the subsoil carbon pool (> 50 % of the soil organic carbon stocks are below 30 cm soil depth). In the Blodgett Forest field warming experiment (California, USA) we investigated how +4 ∘C warming in the whole-soil profile to 100 cm soil depth for 4.5 years has affected the abundance and community structure of microorganisms. We used proxies for bulk microbial biomass carbon (MBC) and functional microbial groups based on lipid biomarkers, such as phospholipid fatty acids (PLFAs) and branched glycerol dialkyl glycerol tetraethers (brGDGTs). With depth, the microbial biomass decreased and the community composition changed. Our results show that the concentration of PLFAs decreased with warming in the subsoil (below 30 cm) by 28 % but was not affected in the topsoil. Phospholipid fatty acid concentrations changed in concert with soil organic carbon. The microbial community response to warming was depth dependent. The relative abundance of Actinobacteria increased in warmed subsoil, and Gram+ bacteria in subsoils adapted their cell membrane structure to warming-induced stress, as indicated by the ratio of anteiso to iso branched PLFAs. Our results show for the first time that subsoil microorganisms can be more affected by warming compared to topsoil microorganisms. These microbial responses could be explained by the observed decrease in subsoil organic carbon concentrations in the warmed plots. A decrease in microbial abundance in warmed subsoils might reduce the magnitude of the respiration response over time. The shift in the subsoil microbial community towards more Actinobacteria might disproportionately enhance the degradation of previously stable subsoil carbon, as this group is able to metabolize complex carbon sources.
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Akari, Maiko, and Yoshitaka Uchida. "Survival Rates of Microbial Communities from Livestock Waste to Soils: A Comparison between Compost and Digestate." Applied and Environmental Soil Science 2021 (January 29, 2021): 1–15. http://dx.doi.org/10.1155/2021/6645203.
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Livestock waste-based products, such as composted manure, are often used in crop production systems. The products’ microbial characteristics differ depending on animal waste treatment methods used (e.g., biogas production/composting). The question remains whether different livestock waste-based products differently impact soil microbiota. A pot experiment with five treatments (control, chemical fertilizer, digestate + chemical fertilizer, wheat straw compost + chemical fertilizer, and woodchip compost + chemical fertilizer) was conducted to compare the survival rates of microbial communities from digestate and composted manure, after their application to agricultural soil. Potatoes were planted in each pot. The changes in soil pH, the concentration of ammonium and nitrate, and the microbial community properties were monitored after 1, 6, 10, and 14 weeks of the application of livestock waste-based products. The application of composted manure, especially woodchip compost, showed a relatively more extensive impact on the soil microbial community structure than the other treatments. Woodchip compost contained a relatively more abundant and diverse bacterial community than digestate, and its family-level bacterial community structure was similar to that of the soil. These characteristics might determine the extent of the impact of livestock waste-based products on soil microbial communities. Digestate markedly influenced the inorganic nitrogen concentrations in soils but did not affect the soil microbial community. In conclusion, the survival rate of microbes of livestock waste-based products varies depending on the product type. Further investigation is needed to fully understand their impact on soils’ microbial functions.
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Di, H. J., G. P. Sparling, R. Lee, and G. N. Magesan. "The effect of mineralisation rates of atrazine in surface and subsurface soils on its groundwater contamination potential." Soil Research 39, no. 1 (2001): 175. http://dx.doi.org/10.1071/sr00004.
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Atrazine is a widely used herbicide for weed control and has been found in groundwater in many countries. The groundwater contamination potential of atrazine in 2 soils on the east coast of the North Island of New Zealand was modelled under 3 scenarios. Scenario 1 used atrazine mineralisation rates as determined in an incubation experiment which showed higher rates of mineralisation in subsoil layers than in surface soils. Scenario 2 assumed a decreasing mineralisation rate with soil depth in proportion to changes in microbial biomass. Scenario 3 used a logistic model to describe atrazine mineralisation rates compared with the first-order model used in Scenarios 1 and 2. The results showed that serious errors could occur when modelling the groundwater contamination potential by assuming a decreasing degradation rates with soil depth, when in fact the degradation rates could be higher in some subsoil layers. A site that had not been exposed to atrazine in the past was shown to have a higher potential for groundwater contamination than a neighbouring site of the same soil which had been treated with atrazine in the past. The groundwater contamination potential was found to be higher in the Te Awa soil than in the Twyford soil due to the longer mineralisation half-lives in the Te Awa soil.
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Edenborn, S. L., A. J. Sexstone, Y. Sutanto, and J. A. Chapman. "Relationships among Contrasting Measurements of Microbial Dynamics in Pasture and Organic Farm Soils." Applied and Environmental Soil Science 2011 (2011): 1–10. http://dx.doi.org/10.1155/2011/537459.
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Soil bacteria exhibit short-term variations in community structure, providing an indication of anthropogenic disturbances. In this study, microbial biomass carbon (MBC), potentially mineralizable nitrogen (PMN), community level physiological profiling (CLPP), and culture-dependent DGGE (CD DGGE) fingerprinting of the 16S rRNA gene were used to compare microbial communities in organic farm and pasture soils subjected to differing agronomic treatments. Correlation analyses revealed significant relationships between MBC, PMN, and data derived from microbial community analyses. All measures separated soil types but varied in their ability to distinguish among treatments within a soil type. Overall, MBC, PMN, and CLPP were most responsive to compost and manure amendments, while CD DGGE resolved differences in legume cropping and inorganic fertilization. The results support the hypothesis that culturable soil bacteria are a responsive fraction of the total microbial community, sensitive to agronomic perturbations and amenable to further studies aimed at linking community structure with soil functions.
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Li, Zhi, Evan Siemann, Bangliang Deng, Shuli Wang, Yu Gao, Xiaojun Liu, Xueling Zhang, Xiaomin Guo, and Ling Zhang. "Soil microbial community responses to soil chemistry modifications in alpine meadows following human trampling." CATENA 194 (November 2020): 104717. http://dx.doi.org/10.1016/j.catena.2020.104717.
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Wojcik, Robin, Johanna Donhauser, Beat Frey, Stine Holm, Alexandra Holland, Alexandre M. Anesio, David A. Pearce, Lucie Malard, Dirk Wagner, and Liane G. Benning. "Linkages between geochemistry and microbiology in a proglacial terrain in the High Arctic." Annals of Glaciology 59, no. 77 (December 2018): 95–110. http://dx.doi.org/10.1017/aog.2019.1.
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ABSTRACTProglacial environments are ideal for studying the development of soils through the changes of rocks exposed by glacier retreat to weathering and microbial processes. Carbon (C) and nitrogen (N) contents as well as soil pH and soil elemental compositions are thought to be dominant factors structuring the bacterial, archaeal and fungal communities in the early stages of soil ecosystem formation. However, the functional linkages between C and N contents, soil composition and microbial community structures remain poorly understood. Here, we describe a multivariate analysis of geochemical properties and associated microbial community structures between a moraine and a glaciofluvial outwash in the proglacial area of a High Arctic glacier (Longyearbreen, Svalbard). Our results reveal distinct differences in developmental stages and heterogeneity between the moraine and the glaciofluvial outwash. We observed significant relationships between C and N contents,δ13Corgandδ15N isotopic ratios, weathering and microbial abundance and community structures. We suggest that the observed differences in microbial and geochemical parameters between the moraine and the glaciofluvial outwash are primarily a result of geomorphological variations of the proglacial terrain.
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Nozawa-Inoue, Mamie, Kate M. Scow, and Dennis E. Rolston. "Reduction of Perchlorate and Nitrate by Microbial Communities in Vadose Soil." Applied and Environmental Microbiology 71, no. 7 (July 2005): 3928–34. http://dx.doi.org/10.1128/aem.71.7.3928-3934.2005.
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ABSTRACT Perchlorate contamination is a concern because of the increasing frequency of its detection in soils and groundwater and its presumed inhibitory effect on human thyroid hormone production. Although significant perchlorate contamination occurs in the vadose (unsaturated) zone, little is known about perchlorate biodegradation potential by indigenous microorganisms in these soils. We measured the effects of electron donor (acetate and hydrogen) and nitrate addition on perchlorate reduction rates and microbial community composition in microcosm incubations of vadose soil. Acetate and hydrogen addition enhanced perchlorate reduction, and a longer lag period was observed for hydrogen (41 days) than for acetate (14 days). Initially, nitrate suppressed perchlorate reduction, but once perchlorate started to be degraded, the process was stimulated by nitrate. Changes in the bacterial community composition were observed in microcosms enriched with perchlorate and either acetate or hydrogen. Denaturing gradient gel electrophoresis analysis and partial sequencing of 16S rRNA genes recovered from these microcosms indicated that formerly reported perchlorate-reducing bacteria were present in the soil and that microbial community compositions were different between acetate- and hydrogen-amended microcosms. These results indicate that there is potential for perchlorate bioremediation by native microbial communities in vadose soil.
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Cartwright, Jennifer, E. Kudjo Dzantor, and Bahram Momen. "Soil microbial community profiles and functional diversity in limestone cedar glades." CATENA 147 (December 2016): 216–24. http://dx.doi.org/10.1016/j.catena.2016.07.010.
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Naylor, Dan, Ryan McClure, and Janet Jansson. "Trends in Microbial Community Composition and Function by Soil Depth." Microorganisms 10, no. 3 (February 28, 2022): 540. http://dx.doi.org/10.3390/microorganisms10030540.
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Microbial communities play important roles in soil health, contributing to processes such as the turnover of organic matter and nutrient cycling. As soil edaphic properties such as chemical composition and physical structure change from surface layers to deeper ones, the soil microbiome similarly exhibits substantial variability with depth, with respect to both community composition and functional profiles. However, soil microbiome studies often neglect deeper soils, instead focusing on the top layer of soil. Here, we provide a synthesis on how the soil and its resident microbiome change with depth. We touch upon soil physicochemical properties, microbial diversity, composition, and functional profiles, with a special emphasis on carbon cycling. In doing so, we seek to highlight the importance of incorporating analyses of deeper soils in soil studies.
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Moore, Anni, Melissa Lenczewski, Rosa Maria Leal-Bautista, and Melvin Duvall. "Groundwater microbial diversity and antibiotic resistance linked to human population density in Yucatan Peninsula, Mexico." Canadian Journal of Microbiology 66, no. 1 (January 2020): 46–58. http://dx.doi.org/10.1139/cjm-2019-0173.
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Microbial community composition in selected karst groundwater sites in the Yucatan Peninsula, Mexico, was assessed to determine the environmental variables influencing groundwater microbial diversity. The karst aquifer system is a groundwater-dependent ecosystem and is the world’s second largest underwater karst cave system. The area’s geology allows precipitation to infiltrate into the groundwater system and prevents accumulation of surface water; as such, groundwater is the only source of fresh water on the peninsula. The sampling locations consisted of three karst sinkholes that extend through the freshwater zone into the saline water, and an abandoned drinking water well of an ocean-side resort, during the dry and rainy seasons. The analysis showed that highly diverse microbial communities are present in the Yucatan groundwater, sustained by permanently warm temperatures and high nutrient input from human activity. Proximity to densely populated areas, such as tourist resorts, is the most important factor influencing both the diversity and presence of fecal bacteria and the antibiotic resistance profile.
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Allison, Victoria J., Zhanna Yermakov, R. Michael Miller, Julie D. Jastrow, and Roser Matamala. "Assessing Soil Microbial Community Composition Across Landscapes: Do Surface Soils Reveal Patterns?" Soil Science Society of America Journal 71, no. 3 (May 2007): 730–34. http://dx.doi.org/10.2136/sssaj2006.0301n.
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Ma, L., C. Guo, X. Lü, S. Yuan, and R. Wang. "Do climate factors govern soil microbial community composition and biomass at a regional scale?" Biogeosciences Discussions 11, no. 12 (December 18, 2014): 17729–56. http://dx.doi.org/10.5194/bgd-11-17729-2014.
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Abstract. Soil microbial communities play important role in organic matter decomposition, nutrient cycling and vegetation dynamic. However, little is known about factors driving soil microbial community composition at large scales. The objective of this study was to determine whether climate dominates among environmental factors governing microbial community composition and biomass at a regional scale. Here, we compared soil microbial communities using phospholipid fatty acid method across 7 land use types from 23 locations in North-East China Transect (850 km x 50 km). The results showed that soil water availability and land use changes exhibited the dominant effects on soil microbial community composition and biomass at the regional scale, while climate factors (expressed as a function of large-scale spatial variation) did not show strong relationships with distribution of microbial community composition. Likewise, factors such as spatial structure, soil texture, nutrient availability and vegetation types were not important. Wetter soils had higher contributions of gram-positive bacteria, whereas drier soils had higher contributions of gram-negative bacteria and fungi. Heavily disturbed soils had lower contributions of gram-negative bacteria and fungi than historically disturbed and undisturbed soils. The lowest microbial biomass appeared in the wettest and driest soils. In conclusion, dominant climate factors, commonly known to structure distribution of macroorganisms, were not the most important drivers governing regional pattern of microbial communities because of inclusion of irrigated and managed practices. In comparison, soil water regime and land use types appear to be primary determinants of microbial community composition and biomass.
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Sipilä, Timo P., Kim Yrjälä, Laura Alakukku, and Ansa Palojärvi. "Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers." Applied and Environmental Microbiology 78, no. 23 (September 14, 2012): 8191–201. http://dx.doi.org/10.1128/aem.02005-12.
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ABSTRACTThe exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities andFusariumfungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses.Fusarium culmorumsoil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P< 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P< 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P< 0.02 for the sum of PLFAs;P< 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy.
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Erktan, Amandine, Matthias C. Rillig, Andrea Carminati, Alexandre Jousset, and Stefan Scheu. "Protists and collembolans alter microbial community composition, C dynamics and soil aggregation in simplified consumer–prey systems." Biogeosciences 17, no. 20 (October 17, 2020): 4961–80. http://dx.doi.org/10.5194/bg-17-4961-2020.
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Abstract. Microbes play an essential role in soil functioning including biogeochemical cycling and soil aggregate formation. Yet, a major challenge is to link microbes to higher trophic levels and assess consequences for soil functioning. Here, we aimed to assess how microbial consumers modify microbial community composition (PLFA markers), as well as C dynamics (microbial C use, SOC concentration and CO2 emission) and soil aggregation. We rebuilt two simplified soil consumer–prey systems: a bacterial-based system comprising amoebae (Acanthamoeba castellanii) feeding on a microbial community dominated by the free-living bacterium Pseudomonas fluorescens and a fungal-based system comprising collembolans (Heteromurus nitidus) grazing on a microbial community dominated by the saprotrophic fungus Chaetomium globosum. The amoeba A. castellanii did not affect microbial biomass and composition, but it enhanced the formation of soil aggregates and tended to reduce their stability. Presumably, the dominance of P. fluorescens, able to produce antibiotic toxins in response to the attack by A. castellanii, was the main cause of the unchanged microbial community composition, and the release of bacterial extracellular compounds, such as long-chained polymeric substances or proteases, in reaction to predation was responsible for the changes in soil aggregation as a side effect. In the fungal system, collembolans significantly modified microbial community composition via consumptive and non-consumptive effects including the transport of microbes on the body surface. As expected, fungal biomass promoted soil aggregation and was reduced in the presence of H. nitidus. Remarkably, we also found an unexpected contribution of changes in bacterial community composition to soil aggregation. In both the bacterial and fungal systems, bacterial and fungal communities mainly consumed C from soil organic matter (rather than the litter added). Increased fungal biomass was associated with an increased capture of C from added litter, and the presence of collembolans levelled off this effect. Neither amoebae nor collembolans altered SOC concentrations and CO2 production. Overall, the results demonstrated that trophic interactions are important for achieving a mechanistic understanding of biological contributions to soil aggregation and may occur without major changes in C dynamics and with or without changes in the composition of the microbial community.
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Zhou, Jizhong, Beicheng Xia, David S. Treves, L. Y. Wu, Terry L. Marsh, Robert V. O’Neill, Anthony V. Palumbo, and James M. Tiedje. "Spatial and Resource Factors Influencing High Microbial Diversity in Soil." Applied and Environmental Microbiology 68, no. 1 (January 2002): 326–34. http://dx.doi.org/10.1128/aem.68.1.326-334.2002.
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ABSTRACT To begin defining the key determinants that drive microbial community structure in soil, we examined 29 soil samples from four geographically distinct locations taken from the surface, vadose zone, and saturated subsurface using a small-subunit rRNA-based cloning approach. While microbial communities in low-carbon, saturated, subsurface soils showed dominance, microbial communities in low-carbon surface soils showed remarkably uniform distributions, and all species were equally abundant. Two diversity indices, the reciprocal of Simpson’s index (1/D) and the log series index, effectively distinguished between the dominant and uniform diversity patterns. For example, the uniform profiles characteristic of the surface communities had diversity index values that were 2 to 3 orders of magnitude greater than those for the high-dominance, saturated, subsurface communities. In a site richer in organic carbon, microbial communities consistently exhibited the uniform distribution pattern regardless of soil water content and depth. The uniform distribution implies that competition does not shape the structure of these microbial communities. Theoretical studies based on mathematical modeling suggested that spatial isolation could limit competition in surface soils, thereby supporting the high diversity and a uniform community structure. Carbon resource heterogeneity may explain the uniform diversity patterns observed in the high-carbon samples even in the saturated zone. Very high levels of chromium contamination (e.g., >20%) in the high-organic-matter soils did not greatly reduce the diversity. Understanding mechanisms that may control community structure, such as spatial isolation, has important implications for preservation of biodiversity, management of microbial communities for bioremediation, biocontrol of root diseases, and improved soil fertility.
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Yoshitake, Shinpei, and Takayuki Nakatsubo. "Changes in soil microbial biomass and community composition along vegetation zonation in a coastal sand dune." Soil Research 46, no. 4 (2008): 390. http://dx.doi.org/10.1071/sr07104.
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We used phospholipid fatty acid (PLFA) analysis to examine the relation of microbial biomass and community composition to vegetation zonation on a coastal sand dune. Soil samples were collected along 3 line transects established from the shoreline to the inland bush. Total PLFA content and PLFA composition of soils were used as indices of total microbial biomass and community composition, respectively. The microbial biomass was much higher in the inland Vitex rotundifolia zone than in the seaside plots. The microbial community composition also differed among the vegetation zones, with a higher contribution of fungal biomarkers in the inland plots. The microbial biomass increased significantly with increasing soil organic matter (SOM) content, but was not correlated with soil salinity. These results suggest that microbial biomass in the coastal sand dune was controlled primarily by the accumulation of SOM. The microbial community composition also changed with SOM content in the seaside plots, but SOM had little effect in the inland plots. These results suggest that the factors limiting the microbial community composition differed with location on the dune.
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Dangi, Sadikshya R., James S. Gerik, Rebecca Tirado-Corbalá, and Husein Ajwa. "Soil Microbial Community Structure and Target Organisms under Different Fumigation Treatments." Applied and Environmental Soil Science 2015 (2015): 1–8. http://dx.doi.org/10.1155/2015/673264.
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Producers of several high-value crops in California rely heavily on soil fumigants to control key diseases, nematodes, and weeds. Fumigants with broad biocidal activity can affect both target and nontarget soil microorganisms. The ability of nontarget soil microorganisms to recover after fumigation treatment is critical because they play an important role in sustaining the health of agricultural and natural soil systems. Fumigation trial was conducted in Parlier, CA, and the study focuses on the effects of different rates of Telone C35 and also methyl bromide fumigation with polyethylene (PE) and totally impermeable film (TIF) tarps on target and nontarget soil microorganisms using field samples. Results indicated that the populations of target organisms, such asFusarium oxysporumandPythiumspp., were reduced at all rates of fumigants. Phospholipid fatty acid (PLFA) analysis indicated that all major nontarget soil microbial groups such as Gram positive bacteria, Gram negative bacteria, fungi, and arbuscular mycorrhizal fungi (AMF) were affected by methyl bromide (MeBr) fumigation treatment. In general, the effects of Telone C35 (299 L/ha) under PE tarp had the least impact on microbial community structure and better effect on controlling target microorganisms and, therefore, indicated the better option among fumigation treatments.
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Zhang, Li, Zhimin Xu, Yajun Sun, Yating Gao, and Lulu Zhu. "Coal Mining Activities Driving the Changes in Microbial Community and Hydrochemical Characteristics of Underground Mine Water." International Journal of Environmental Research and Public Health 19, no. 20 (October 16, 2022): 13359. http://dx.doi.org/10.3390/ijerph192013359.
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Coal mining can cause groundwater pollution, and microorganism may reflect/affect its hydrochemical characteristics, yet little is known about the microorganism’s distribution characteristics and its influence on the formation and evolution of mine water quality in underground coal mines. Here, we investigated the hydrochemical characteristics and microbial communities of six typical zones in a typical North China coalfield. The results showed that hydrochemical compositions and microbial communities of the water samples displayed apparent zone-specific patterns. The microbial community diversity of the six zones followed the order of surface waters > coal roadways > water sumps ≈ rock roadways ≈ goafs > groundwater aquifers. The microbial communities corresponded to the redox sensitive indices’ levels. Coal roadways and goafs were the critical zones of groundwater pollution prevention and control. During tunneling in the panel, pyrite was oxidized by sulfur-oxidizing bacteria leading to SO42− increase. With the closure of the panel and formation of the goaf, SO42− increased rapidly for a short period. However, with the time since goaf closure, sulfate-reducing bacteria (e.g., c_Thermodesulfovibrionia, Desulfobacterium_catecholicum, etc.) proportion increased significantly, leading to SO42− concentration’s decrease by 42% over 12 years, indicating the long-term closed goafs had a certain self-purification ability. These findings would benefit mine water pollution prevention and control by district.
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Ma, L., C. Guo, X. Lü, S. Yuan, and R. Wang. "Soil moisture and land use are major determinants of soil microbial community composition and biomass at a regional scale in northeastern China." Biogeosciences 12, no. 8 (April 30, 2015): 2585–96. http://dx.doi.org/10.5194/bg-12-2585-2015.
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Abstract. Global environmental factors impact soil microbial communities and further affect organic matter decomposition, nutrient cycling and vegetation dynamic. However, little is known about the relative contributions of climate factors, soil properties, vegetation types, land management practices and spatial structure (which serves as a proxy for underlying effects of temperature and precipitation for spatial variation) on soil microbial community composition and biomass at large spatial scales. Here, we compared soil microbial communities using phospholipid fatty acid method across 7 land use types from 23 locations at a regional scale in northeastern China (850 × 50 km). The results showed that soil moisture and land use changes were most closely related to microbial community composition and biomass at the regional scale, while soil total C content and climate effects were weaker but still significant. Factors such as spatial structure, soil texture, nutrient availability and vegetation types were not important. Higher contributions of gram-positive bacteria were found in wetter soils, whereas higher contributions of gram-negative bacteria and fungi were observed in drier soils. The contributions of gram-negative bacteria and fungi were lower in heavily disturbed soils than historically disturbed and undisturbed soils. The lowest microbial biomass appeared in the wettest and driest soils. In conclusion, dominant climate and soil properties were not the most important drivers governing microbial community composition and biomass because of inclusion of irrigated and managed practices, and thus soil moisture and land use appear to be primary determinants of microbial community composition and biomass at the regional scale in northeastern China.
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Sivaram, Anithadevi Kenday, Logeshwaran Panneerselvan, Kannappar Mukunthan, and Mallavarapu Megharaj. "Effect of Pyroligneous Acid on the Microbial Community Composition and Plant Growth-Promoting Bacteria (PGPB) in Soils." Soil Systems 6, no. 1 (January 14, 2022): 10. http://dx.doi.org/10.3390/soilsystems6010010.
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Pyroligneous acid (PA) is often used in agriculture as a plant growth and yield enhancer. However, the influence of PA application on soil microorganisms is not often studied. Therefore, in this study, we investigated the effect of PA (0.01–5% w/w in soil) on the microbial diversity in two different soils. At the end of eight weeks of incubation, soil microbial community dynamics were determined by Illumina-MiSeq sequencing of 16S rRNA gene amplicons. The microbial composition differed between the lower (0.01% and 0.1%) and the higher (1% and 5%) concentration in both PA spiked soils. The lower concentration of PA resulted in higher microbial diversity and dehydrogenase activity (DHA) compared to the un-spiked control and the soil spiked with high PA concentrations. Interestingly, PA-induced plant growth-promoting bacterial (PGPB) genera include Bradyrhizobium, Azospirillum, Pseudomonas, Mesorhizobium, Rhizobium, Herbaspiriluum, Acetobacter, Beijerinckia, and Nitrosomonas at lower concentrations. Additionally, the PICRUSt functional analysis revealed the predominance of metabolism as the functional module’s primary component in both soils spiked with 0.01% and 0.1% PA. Overall, the results elucidated that PA application in soil at lower concentrations promoted soil DHA and microbial enrichment, particularly the PGPB genera, and thus have great implications for improving soil health.
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Aislabie, Jackie, Malcolm McLeod, Janine Ryburn, Alexandra McGill, and Daniel Thornburrow. "Soil type influences the leaching of microbial indicators under natural rainfall following application of dairy shed effluent." Soil Research 49, no. 3 (2011): 270. http://dx.doi.org/10.1071/sr10147.
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The ability of soil to function as a barrier between microbial pathogens in wastes and groundwater following application of animal wastes is dependent on soil structure. We irrigated soil lysimeters with dairy shed effluent at intervals of 3–4 months and monitored microbial indicators (somatic coliphage, faecal enterococci, Escherichia coli) in soil core leachates for 1 year. The lysimeters were maintained in a lysimeter facility under natural soil temperature and moisture regimes. Microbial indicators were rapidly transported to depth in well-structured Netherton clay loam soil. Peak concentrations of E. coli and somatic coliphage were detected immediately following dairy shed effluent application to Netherton clay loam soil, and E. coli continued to leach from the soil following rainfall. In contrast, microbial indicators were rarely detected in leachates from fine-structured Manawatu sandy loam soil. Potential for leaching was dependent on soil moisture conditions in Manawatu soil but not Netherton soil, where leaching occurred regardless. Dye studies confirmed that E. coli can be transported to depth by flow through continuous macropores in Netherton soils. However, in the main E. coli was retained in topsoil of Netherton and Manawatu soil.
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Dangi, Sadikshya R., Peter D. Stahl, Abbey F. Wick, Lachlan J. Ingram, and Jeffrey S. Buyer. "Soil Microbial Community Recovery in Reclaimed Soils on a Surface Coal Mine Site." Soil Science Society of America Journal 76, no. 3 (May 2012): 915–24. http://dx.doi.org/10.2136/sssaj2011.0288.
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Rahman, Khondaker Md Jaminur, Farzana Diba, Md Sadikur Rahman Shuvo, Mohammad Anwar Siddique, M. Anwar Hossain, and Munawar Sultana. "Metagenomic investigation of bacterial community of arsenic-prone area in the northwest region of Bangladesh." Bangladesh Journal of Microbiology 39, no. 1 (January 22, 2023): 31–38. http://dx.doi.org/10.3329/bjm.v39i1.64056.
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Metagenomic analysis provides in-depth understanding of microbe mediated Arsenic (As) metabolism. The present study aims atmetagenomic analysis of the distribution, diversity, and abundance of bacteriome in arsenic affected groundwater and surrounding soils collected fromBogra district of Bangladesh. Metagenomic DNA was extracted from two groundwater samples BCW3 andBCW4 (As content10μgL-1 and 500 μgL-1, respectively), and two tube-well surrounding soil samples BSS1 and BCS5 (As content335 μgkg-1 and 492 μgkg-1),where As rich water flows off. Metagenomic analysis of six hypervariable regions of 16S rRNA gene resulted in a total of 788709 processed sequence reads and 5878 operational taxonomic units (OTUs). Bacterial richness, abundance and diversity (alpha and beta) were higher in BCW4 (85 genera) than BCW3 (19 genera) whereas both soil samples exhibited almost similar richness and diversity. Predominant genera in BCW3 were Pseudomonas, Microbacterium, Achromobacterwhereas Acinetobacter, Thiothrix, Stenotrophomonas, Paracoccus, Dechloromonas dominated in BCW4. Soils were co-dominated with more than hundreds of genera with a high relative abundance of Bacillus, Rhodoplanesand Pseudomonas.Metagenomic investigation explored potentialarsenotrophicbacteriome. Exploring microbial community might help to understand the biogeochemistry of As affected groundwater and surrounding soil environment.
Bangladesh J Microbiol, Volume 39, Number 1, June 2022, pp 31-38
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Che, Zihan, Deyong Yu, Kelong Chen, Hengsheng Wang, Ziwei Yang, Fumei Liu, and Xia Wang. "Effects of Warming on Microbial Community Characteristics in the Soil Surface Layer of Niaodao Wetland in the Qinghai Lake Basin." Sustainability 14, no. 22 (November 17, 2022): 15255. http://dx.doi.org/10.3390/su142215255.
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Lakeshore wetlands are important terrestrial ecosystems worldwide, and the lakeshore wetlands of the Tibetan Plateau are sensitive to climate change. Therefore, in the context of global warming, studying the effects of temperature rise on surface soil microbial communities is essential for wetland biodiversity conservation. In this study, we used metagenomic sequencing to examine changes in the structure of surface soil microbial communities and their metabolic pathways in the Niaodao lakeshore wetland (NLW) in Qinghai Lake at 1.2 °C warming. Under natural control and warming conditions, Proteobacteria and Actinobacteria were the most dominant bacterial phyla, and Ascomycota and Basidiomycota were the predominant fungal phyla. Soil pH, electrical conductivity, and temperature affected the relative abundances of the dominant soil microbes. Effect size estimation in a linear discriminant analysis revealed 11 differential pathways between warming and natural conditions. Warming considerably enhanced the peptidoglycan biosynthetic pathways but inhibited the ATP-binding cassette transporter pathway. Warming treatment affected α-diversity indices, with an increase in the Shannon, Chao1, and richness indices and a decrease in the Simpson index compared with the index changes for the natural control conditions. Analysis of similarities showed significant differences between warming and control samples. Overall, temperature rise altered surface soil microbial community structure and increased surface soil microbial diversity and abundance in NLW.
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Hamamoto, Toru, Meki Chirwa, Imasiku Nyambe, and Yoshitaka Uchida. "Small-Scale Variability in the Soil Microbial Community Structure in a Semideveloped Farm in Zambia." Applied and Environmental Soil Science 2018 (2018): 1–6. http://dx.doi.org/10.1155/2018/7939123.
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The conversion of natural lands into agricultural lands can lead to changes in the soil microbial community structure which, in turn, can affect soil functions. However, few studies have examined the effect of land use changes on the soil microbial community structure in sub-Saharan Africa. Therefore, the aim of this research was to investigate the relationships among soil characteristics and microbial communities in natural and agricultural ecosystems in a semideveloped lowland farm in the central region of Zambia, within which small-scale wetlands had been partly developed as watermelon (Citrullus lanatus) and/or maize (Zea mays) farms. We sampled soils from four different land use types within this farm: “native forest,” “grassland,” “watermelon farm,” and “maize farm.” We found that the land use type had a significant effect on the soil bacterial community structure at the class level, with the class Bacilli having significantly higher relative abundances in the forest sites and Gammaproteobacteria having significantly higher relative abundances in the maize sites than in the other land use types. These findings indicate that these bacterial classes may be sensitive to changes in soil ecosystems, and so further studies are required to investigate microbial indicators for the sustainable development of wetlands in sub-Saharan Africa.
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Liao, Jianli, Qicong Xu, Huilian Xu, and Danfeng Huang. "Natural Farming Improves Soil Quality and Alters Microbial Diversity in a Cabbage Field in Japan." Sustainability 11, no. 11 (June 3, 2019): 3131. http://dx.doi.org/10.3390/su11113131.
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Natural farming (NF), an environmentally friendly agricultural practice similar to organic farming, was developed in Japan. Unlike conventional farming, little is known about the influence of NF on soil microbial communities, especially the surface soil. We therefore compared the effect of seven years’ conventional practice (CP), conventional practice without chemicals (CF), and NF on soil properties and microbial community structure at two soil depths (0–10, 10–20 cm) in an experimental cabbage field. Both soil depth and agricultural practice significantly influenced edaphic measures and microbial community structure. NF improved bulk density, pH, electrical conductivity, urease activity, and nitrate reductase activity in topsoil; similar trends were observed in deeper soil. Pyrosequencing demonstrated that the use of pesticides in conventional farming (CP) led to lower microbial abundance and diversity in topsoil than CF. Similarly, NF increased microbial abundance compared to CP. However, distinct taxa were present in the topsoil, but not deeper soil, in each treatment. CP-enriched microbial genera may be related to plant pathogens (e.g., Erwinia and Brenneria) and xenobiotic degraders (e.g., Sphingobacterium and Comamonas). The microbial community structure of NF was distinct to CP/CF, with enrichment of Pedomicrobium and Solirubrobacter, which may prefer stable soil conditions. Network analysis of dominant genera confirmed the more stable, complex microbial network structure of the 0–10 cm than 10–20 cm layer. Flavisolibacter/Candidatus Solibacter and Candidatus Nitrososphaera/Leuconostoc are potentially fundamental taxa in the 0–10 cm and 10–20 cm layer networks, respectively. Overall, we show that NF positively affects soil quality and microbial community composition within sustainable farming systems.
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Balasooriya, W. K., K. Denef, J. Peters, N. E. C. Verhoest, and P. Boeckx. "Vegetation composition and soil microbial community structural changes along a wetland hydrological gradient." Hydrology and Earth System Sciences 12, no. 1 (February 26, 2008): 277–91. http://dx.doi.org/10.5194/hess-12-277-2008.
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Abstract. Fluctuations in wetland hydrology create an interplay between aerobic and anaerobic conditions, controlling vegetation composition and microbial community structure and activity in wetland soils. In this study, we investigated the vegetation composition and microbial community structural and functional changes along a wetland hydrological gradient. Two different vegetation communities were distinguished along the hydrological gradient; Caricetum gracilis at the wet depression and Arrhenatheretum elatioris at the drier upper site. Microbial community structural changes were studied by a combined in situ 13CO2 pulse labeling and phospholipid fatty acid (PLFA) based stable isotope probing approach, which identifies the microbial groups actively involved in assimilation of newly photosynthesized, root-derived C in the rhizosphere soils. Gram negative bacterial communities were relatively more abundant in the surface soils of the drier upper site than in the surface soils of the wetter lower site, while the lower site and the deeper soil layers were relatively more inhabited by gram positive bacterial communities. Despite their large abundance, the metabolically active proportion of gram positive bacterial and actinomycetes communities was much smaller at both sites, compared to that of the gram negative bacterial and fungal communities. This suggests much slower assimilation of root-derived C by gram positive and actinomycetes communities than by gram negative bacteria and fungi at both sites. Ground water depth showed a significant effect on the relative abundance of several microbial communities. Relative abundance of gram negative bacteria significantly decreased with increasing ground water depth while the relative abundance of gram positive bacteria and actinomycetes at the surface layer increased with increasing ground water depth.