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.

2009 ◽  
Vol 55 (1) ◽  
pp. 12-20 ◽  
Author(s):  
J. Aislabie ◽  
J. Ryburn ◽  
A. Sarmah
Keyword(s):  
Heterotrophic Bacteria ◽  
Soil Microbial Communities ◽  
Shallow Groundwater ◽  
Soil Surface ◽  
Soil Microbial ◽  
Nitrate Reducers ◽  
Groundwater Samples ◽  
In Situ Conditions ◽  
Terrestrial Water ◽  
Ornithogenic Soil

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.

scholarly journals Role of Plant Residues in Determining Temporal Patterns of the Activity, Size, and Structure of Nitrate Reducer Communities in Soil

2010 ◽  
Vol 76 (21) ◽  
pp. 7136-7143 ◽  
Author(s):  
D. Chèneby ◽  
D. Bru ◽  
N. Pascault ◽  
P. A. Maron ◽  
L. Ranjard ◽  
...  
Keyword(s):  
Microbial Community ◽  
Nitrate Reduction ◽  
Soil Microbial Communities ◽  
Fold Increase ◽  
N Cycling ◽  
Plant Residue ◽  
Plant Residues ◽  
Soil Microbial ◽  
Reduction Activity ◽  
Nitrate Reducers

ABSTRACT The incorporation of plant residues into soil not only represents an opportunity to limit soil organic matter depletion resulting from cultivation but also provides a valuable source of nutrients such as nitrogen. However, the consequences of plant residue addition on soil microbial communities involved in biochemical cycles other than the carbon cycle are poorly understood. In this study, we investigated the responses of one N-cycling microbial community, the nitrate reducers, to wheat, rape, and alfalfa residues for 11 months after incorporation into soil in a field experiment. A 20- to 27-fold increase in potential nitrate reduction activity was observed for residue-amended plots compared to the nonamended plots during the first week. This stimulating effect of residues on the activity of the nitrate-reducing community rapidly decreased but remained significant over 11 months. During this period, our results suggest that the potential nitrate reduction activity was regulated by both carbon availability and temperature. The presence of residues also had a significant effect on the abundance of nitrate reducers estimated by quantitative PCR of the narG and napA genes, encoding the membrane-bound and periplasmic nitrate reductases, respectively. In contrast, the incorporation of the plant residues into soil had little impact on the structure of the narG and napA nitrate-reducing community determined by PCR-restriction fragment length polymorphism (RFLP) fingerprinting. Overall, our results revealed that the addition of plant residues can lead to important long-term changes in the activity and size of a microbial community involved in N cycling but with limited effects of the type of plant residue itself.

scholarly journals Microbial Biobanking Cyanobacteria-rich topsoil facilitates mine rehabilitation

2017 ◽  
Author(s):  
Wendy Williams ◽  
Mel Schneemilch ◽  
Angela Chilton ◽  
Stephen Williams ◽  
Brett Neilan
Keyword(s):  
Ecosystem Function ◽  
Effective Means ◽  
Monitoring Program ◽  
Soil Microbial Communities ◽  
Soil Surface ◽  
Arid Environment ◽  
Soil Restoration ◽  
Soil Microbial ◽  
Community Profiling ◽  
Mining Rehabilitation

Abstract. Mining rehabilitation requires key solutions to complex issues relating to ecosystem function. In arid landscapes, the removal or disturbance of topsoil incorporating soil microbial communities can result in a shift in ecosystem function. Soil surfaces in arid regions are protected by biocrusts that regulate soil moisture, sequester carbon and fix significant quantities of atmospheric nitrogen. Cyanobacteria often dominate these bioactive surfaces and work as ecosystem engineers in that they are in sufficiently large quantities they initiate biocrust establishment and facilitate soil surface stabilisation. Cyanobacterial exopolymeric secretions form cohesive and protective layers at the soil surface that minimise wind erosion. This research encompassed soil microbial community profiling (using a polyphasic approach) with a focus on biobanking topsoil for rehabilitation purposes. The research was in collaboration with Iluka Resources at Jacinth–Ambrosia (J–A) mineral sand mine located in a semi-arid chenopod shrubland in southern Australia. At J–A diverse biocrusts included a significant representation of cyanobacteria, lichens and mosses that inhabited nearly half of all soil surfaces. Cyanobacterial community structure at J–A was comprised of a variety of species having a range of attributes that contributed to their resilience and survival in an arid environment. Stockpiling from shallow scrapings and storage at low profiles appeared beneficial in microbial biobanking cyanobacterial inoculum that would facilitate recovery over time. These studies have provided information for the establishment of a monitoring program that assesses the re-establishment of biocrusts following mining. Following soil stockpiling that occurred during the mining process, cyanobacterial taxa recovered at different rates. Cyanobacterial strategies central to survival include exopolymeric production, spectral adaptation, nitrogen fixation and motility. Biocrust re-establishment during mining rehabilitation relies on the role of cyanobacteria as a means of early soil stabilisation. Provided there is adequate cyanobacterial inoculum in the topsoil stockpiles their growth and the subsequent crust formation should take place largely unassisted. Ongoing monitoring of biocrust recovery is important as it provides an effective means of measuring important soil restoration processes.

scholarly journals Specific features of soil microbial communities under Lavandula angustifolia Mill. introduced plants

2015 ◽  
Vol 16 (1-2) ◽  
pp. 66-74
Author(s):  
O. P. Yunosheva ◽  
N. E. Ellanska
Keyword(s):  
Organic Matter ◽  
Soil Moisture ◽  
Organic Nitrogen ◽  
Heterotrophic Bacteria ◽  
Soil Microbial Communities ◽  
Comparative Characteristic ◽  
Soil Conditions ◽  
Forest Steppe ◽  
Lavandula Angustifolia ◽  
Soil Microbial

In article the results of microbiological studies of Lavandula angustifolia Mill introductive plants soil are presented. The purpose of this study was to investigate the influence of hydrothermal and soil conditions of forest steppe zone on the microbial cenosis formation and dynamics of taxonomic and ecology-trophic groups of microorganisms. 9–10 years age plants L. angustifolia (Yuzhnoberezhnaja and Record varieties) have been studied during two years on the experimental fields of the National Botanical Garden. Rhizosphere and rows-space soil were taken for experimental researches. Investigations were carried out by conventional microbiology methods – seeding of certain dilutions of soil suspension on selective culture medium. The comparative characteristic of microbial groups was investigated in dynamic according to the lavenders development phases. The decreasing of quantity of soil micromycetes were found during flowering phase in parallel with increasing of their species diversity. It should be noted that compared to control, the lavenders’ rhizosphere differ wider range of micromycetes species that belongs to Trichoderma, Penicillium and, especially, Aspergillus genus. The largest quantity of actinomicetes was observed at the beginning of vegetation. The development of actinomycetes and nitrogen transforming microorganisms depended on soil hydrothermal conditions. We observe decreasing of their quantity during deficiency of soil moisture. The numbers of spore-forming bacteria were significantly increased during the flowering period. Compared to control, the number of cellulozolytic microorganisms increased during intensive vegetation, whereas its highest activity was observed at the end of vegetation. Lavandula angustifolia exametabolites positively influenced to the development of heterotrophic bacteria in the beginning of vegetation, as well as during the flowering, whereas at the end of vegetation we observe the decreasing of its quantity. In opposite, the number of oligonitrophylus microorganisms decreased during the active vegetation, especially during dry period. The correlation between organic nitrogen and non-organic nitrogen consumption microorganisms define process of humus formation. We observed that the processes of organic matter development were fairly balanced. The accumulation of soil organic matter dominated during active vegetation, whereas activation of mineralization processes occurred at the end of vegetation period. Microorganisms’ content was higher in rows-spacing of plants, where concentration of exometabolites was lower. The dynamic of microbial cenosis and direction of microbiological processes have been similar in soil of two researched varieties, but the total number of microorganisms was higher in near-root soil of Yuzhnoberezhnaya variety. The Lavandula angustifolia soil microbial cenosis forms under influence of its plants excretions, in particular essential oils, that have a specific effect on the microflora and cause a quantity decrease of basic groups of microorganisms. The concentration of lavender exometabolites decrease in parallel with increasing of soil moisture and accordingly inhibitory effect of essential oil changes on stimulation. The understanding of soil microbial coenosis formation features will promote prognostication of interrelations between microbiota and plants. It will help to create sustainable landscape compositions and rational use them in making healthy ecosystems and other practical aspects.

scholarly journals Fine-Scale Spatial Structure of Soil Microbial Communities in Burrows of a Keystone Rodent Following Mass Mortality

2021 ◽  
Vol 9 ◽  
Author(s):  
Chadwick Kaufmann ◽  
Loren Cassin-Sackett
Keyword(s):  
Microbial Communities ◽  
Phylogenetic Diversity ◽  
Soil Microbial Communities ◽  
Soil Surface ◽  
Mass Mortality ◽  
Ground Squirrels ◽  
Community Diversity ◽  
Prairie Dogs ◽  
16S Sequencing ◽  
Soil Microbial

Soil microbial communities both reflect and influence biotic and abiotic processes occurring at or near the soil surface. Ecosystem engineers that physically alter the soil surface, such as burrowing ground squirrels, are expected to influence the distribution of soil microbial communities. Black-tailed prairie dogs (Cynomys ludovicianus) construct complex burrows in which activities such as nesting, defecating, and dying are partitioned spatially into different chambers. Prairie dogs also experience large-scale die-offs due to sylvatic plague, caused by the bacterium Yersinia pestis, which lead to mass mortality events with potential repercussions on microbial communities. We used 16S sequencing to examine microbial communities in soil that was excavated by prairie dogs from different burrow locations, and surface soil that was used in the construction of burrow entrances, in populations that experienced plague die-offs. Following the QIIME2 pipeline, we assessed microbial diversity at several taxonomic levels among burrow regions. To do so, we computed community similarity metrics (Bray–Curtis, Jaccard, and weighted and unweighted UniFrac) among samples and community diversity indexes (Shannon and Faith phylogenetic diversity indexes) within each sample. Microbial communities differed across burrow regions, and several taxa exhibited spatial variation in relative abundance. Microbial ecological diversity (Shannon index) was highest in soil recently excavated from within burrows and soils associated with dead animals, and was lowest in soils associated with scat. Phylogenetic diversity varied only marginally within burrows, but the trends paralleled those for Shannon diversity. Yersinia was detected in four samples from one colony, marking the first time the genus has been sampled from soil on prairie dog colonies. The presence of Yersinia was a significant predictor of five bacterial families and eight microbial genera, most of which were rare taxa found in higher abundance in the presence of Yersinia, and one of which, Dictyostelium, has been proposed as an enzootic reservoir of Y. pestis. This study demonstrates that mammalian modifications to soil structure by physical alterations and by mass mortality can influence the distribution and diversity of microbial communities.

An Investigation of the Quantity, Quality and Sources of Groundwater Seepage into the St. Clair River near Sarnia, Ontario, Canada

1986 ◽  
Vol 21 (3) ◽  
pp. 351-367 ◽  
Author(s):  
Michael Sklash ◽  
Sharon Mason ◽  
Suzanne Scott ◽  
Chris Pugsley
Keyword(s):  
Electrical Conductivity ◽  
River Water ◽  
Organic Contaminants ◽  
Shallow Groundwater ◽  
Seepage Rate ◽  
Groundwater Seepage ◽  
Seepage Meters ◽  
Groundwater Samples ◽  
Hydraulic Gradients ◽  
Unidentified Source

Abstract We used seepage meters and minipiezometers to survey a 100 m by 7 km band of streambed of the St. Clair River near Sarnia, Ontario, Canada, to determine the quantity, quality, and sources of groundwater seepage into the river. The average observed seepage rate, 1.4 x 10−8 m3/s/m2, suggests higher than expected hydraulic conductivities and/or hydraulic gradients in the streambed. We found detectable levels of some organic contaminants in streambed groundwater samples from 1.0 and 1.5 m depths, however , concentrations did not exceed drinking water guidelines. Our isotopic and electrical conductivity data indicate that: (l) the streambed groundwater is not just river water, (2) groundwater from the “freshwater aquifer” at the base of the overburden Is not a significant component of the streambed groundwater, (3) some of the streambed groundwater is partially derived from a shallow groundwater flow system, and (4) an unidentified source of water with low tritium, river water-like δ18O, and very high electrical conductivity, contributes to the streambed groundwater.

scholarly journals Distinct Biogeographic Patterns for Archaea, Bacteria, and Fungi along the Vegetation Gradient at the Continental Scale in Eastern China

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Bin Ma ◽  
Zhongmin Dai ◽  
Haizhen Wang ◽  
Melissa Dsouza ◽  
Xingmei Liu ◽  
...  
Keyword(s):  
Eastern China ◽  
Soil Microbial Communities ◽  
Natural Forest ◽  
Community Diversity ◽  
Biogeographic Patterns ◽  
Soil Microbial ◽  
Continental Scale ◽  
Forest Sites ◽  
Vegetation Gradient ◽  
Bacteria And Fungi

ABSTRACT Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. The natural forest ecosystem in Eastern China, from tropical forest to boreal forest, has declined due to cropland development during the last 300 years, yet little is known about the historical biogeographic patterns and driving processes for the major domains of microorganisms along this continental-scale natural vegetation gradient. We predicted the biogeographic patterns of soil archaeal, bacterial, and fungal communities across 110 natural forest sites along a transect across four vegetation zones in Eastern China. The distance decay relationships demonstrated the distinct biogeographic patterns of archaeal, bacterial, and fungal communities. While historical processes mainly influenced bacterial community variations, spatially autocorrelated environmental variables mainly influenced the fungal community. Archaea did not display a distance decay pattern along the vegetation gradient. Bacterial community diversity and structure were correlated with the ratio of acid oxalate-soluble Fe to free Fe oxides (Feo/Fed ratio). Fungal community diversity and structure were influenced by dissolved organic carbon (DOC) and free aluminum (Ald), respectively. The role of these environmental variables was confirmed by the correlations between dominant operational taxonomic units (OTUs) and edaphic variables. However, most of the dominant OTUs were not correlated with the major driving variables for the entire communities. These results demonstrate that soil archaea, bacteria, and fungi have different biogeographic patterns and driving processes along this continental-scale natural vegetation gradient, implying different community assembly mechanisms and ecological functions for archaea, bacteria, and fungi in soil ecosystems. IMPORTANCE Understanding biogeographic patterns is a precursor to improving our knowledge of the function of microbiomes and to predicting ecosystem responses to environmental change. Using natural forest soil samples from 110 locations, this study is one of the largest attempts to comprehensively understand the different patterns of soil archaeal, bacterial, and fungal biogeography at the continental scale in eastern China. These patterns in natural forest sites could ascertain reliable soil microbial biogeographic patterns by eliminating anthropogenic influences. This information provides guidelines for monitoring the belowground ecosystem’s decline and restoration. Meanwhile, the deviations in the soil microbial communities from corresponding natural forest states indicate the extent of degradation of the soil ecosystem. Moreover, given the association between vegetation type and the microbial community, this information could be used to predict the long-term response of the underground ecosystem to the vegetation distribution caused by global climate change. Author Video: An author video summary of this article is available.

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