scholarly journals A rather dry subject; investigating the study of arid-associated microbial communities

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Peter Osborne ◽  
Lindsay J. Hall ◽  
Noga Kronfeld-Schor ◽  
David Thybert ◽  
Wilfried Haerty
Keyword(s):  
Microbial Communities ◽  
Land Surface ◽  
Animal Species ◽  
Arid Environment ◽  
Harsh Environments ◽  
Arid Environments ◽  
Microbial Life ◽  
Microbial Ecosystems ◽  
Limited Food ◽  
Extremes Of Temperature

AbstractAlmost one third of Earth’s land surface is arid, with deserts alone covering more than 46 million square kilometres. Nearly 2.1 billion people inhabit deserts or drylands and these regions are also home to a great diversity of plant and animal species including many that are unique to them. Aridity is a multifaceted environmental stress combining a lack of water with limited food availability and typically extremes of temperature, impacting animal species across the planet from polar cold valleys, to Andean deserts and the Sahara. These harsh environments are also home to diverse microbial communities, demonstrating the ability of bacteria, fungi and archaea to settle and live in some of the toughest locations known. We now understand that these microbial ecosystems i.e. microbiotas, the sum total of microbial life across and within an environment, interact across both the environment, and the macroscopic organisms residing in these arid environments. Although multiple studies have explored these microbial communities in different arid environments, few studies have examined the microbiota of animals which are themselves arid-adapted. Here we aim to review the interactions between arid environments and the microbial communities which inhabit them, covering hot and cold deserts, the challenges these environments pose and some issues arising from limitations in the field. We also consider the work carried out on arid-adapted animal microbiotas, to investigate if any shared patterns or trends exist, whether between organisms or between the animals and the wider arid environment microbial communities. We determine if there are any patterns across studies potentially demonstrating a general impact of aridity on animal-associated microbiomes or benefits from aridity-adapted microbiomes for animals. In the context of increasing desertification and climate change it is important to understand the connections between the three pillars of microbiome, host genome and environment.

scholarly journals CaptureSeq: Hybridization-Based Enrichment of cpn60 Gene Fragments Reveals the Community Structures of Synthetic and Natural Microbial Ecosystems

2021 ◽  
Vol 9 (4) ◽  
pp. 816
Author(s):  
Matthew G. Links ◽  
Tim J. Dumonceaux ◽  
E. Luke McCarthy ◽  
Sean M. Hemmingsen ◽  
Edward Topp ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Dna Sequences ◽  
Pcr Amplification ◽  
Shotgun Sequencing ◽  
Natural Ecosystems ◽  
Gene Markers ◽  
Microbial Profile ◽  
Microbial Ecosystems ◽  
Pcr Targeting

Background. The molecular profiling of complex microbial communities has become the basis for examining the relationship between the microbiome composition, structure and metabolic functions of those communities. Microbial community structure can be partially assessed with “universal” PCR targeting taxonomic or functional gene markers. Increasingly, shotgun metagenomic DNA sequencing is providing more quantitative insight into microbiomes. However, both amplicon-based and shotgun sequencing approaches have shortcomings that limit the ability to study microbiome dynamics. Methods. We present a novel, amplicon-free, hybridization-based method (CaptureSeq) for profiling complex microbial communities using probes based on the chaperonin-60 gene. Molecular profiles of a commercially available synthetic microbial community standard were compared using CaptureSeq, whole metagenome sequencing, and 16S universal target amplification. Profiles were also generated for natural ecosystems including antibiotic-amended soils, manure storage tanks, and an agricultural reservoir. Results. The CaptureSeq method generated a microbial profile that encompassed all of the bacteria and eukaryotes in the panel with greater reproducibility and more accurate representation of high G/C content microorganisms compared to 16S amplification. In the natural ecosystems, CaptureSeq provided a much greater depth of coverage and sensitivity of detection compared to shotgun sequencing without prior selection. The resulting community profiles provided quantitatively reliable information about all three domains of life (Bacteria, Archaea, and Eukarya) in the different ecosystems. The applications of CaptureSeq will facilitate accurate studies of host-microbiome interactions for environmental, crop, animal and human health. Conclusions: cpn60-based hybridization enriched for taxonomically informative DNA sequences from complex mixtures. In synthetic and natural microbial ecosystems, CaptureSeq provided sequences from prokaryotes and eukaryotes simultaneously, with quantitatively reliable read abundances. CaptureSeq provides an alternative to PCR amplification of taxonomic markers with deep community coverage while minimizing amplification biases.

scholarly journals Multicellular and unicellular responses of microbial biofilms to stress

2020 ◽  
Vol 401 (12) ◽  
pp. 1365-1374
Author(s):  
Daniel K.H. Rode ◽  
Praveen K. Singh ◽  
Knut Drescher
Keyword(s):  
Microbial Communities ◽  
Stress Responses ◽  
Spatial Scales ◽  
Organizational Level ◽  
Internal Stresses ◽  
Microbial Life ◽  
Microbial Biofilms ◽  
Applied Stresses

AbstractBiofilms are a ubiquitous mode of microbial life and display an increased tolerance to different stresses. Inside biofilms, cells may experience both externally applied stresses and internal stresses that emerge as a result of growth in spatially structured communities. In this review, we discuss the spatial scales of different stresses in the context of biofilms, and if cells in biofilms respond to these stresses as a collection of individual cells, or if there are multicellular properties associated with the response. Understanding the organizational level of stress responses in microbial communities can help to clarify multicellular functions of biofilms.

scholarly journals Desiccation-crack-induced salinization in deep clay sediment

2012 ◽  
Vol 9 (11) ◽  
pp. 13155-13189
Author(s):  
S. Baram ◽  
Z. Ronen ◽  
D. Kurtzman ◽  
C. Küells ◽  
O. Dahan
Keyword(s):  
Isotopic Composition ◽  
Conceptual Model ◽  
Pore Water ◽  
Vadose Zone ◽  
Land Surface ◽  
Water Infiltration ◽  
Arid Environments ◽  
Desiccation Cracks ◽  
The Impact ◽  
Desiccation Crack

Abstract. A study on water infiltration and solute transport in a clayey vadose zone underlying a dairy farm waste source was conducted to assess the impact of desiccation cracks on subsurface evaporation and salinization. The study is based on five years of continuous measurements of the temporal variation in the vadose zone water-content and on the chemical and isotopic composition of the sediment and pore-water in it. The isotopic composition of water stable isotopes (δ18O and δ2H) in water and sediment samples, from the area where desiccation crack networks prevail, indicated subsurface evaporation down to ∼3.5 m below land surface, and vertical and lateral preferential transport of water, following erratic preferential infiltration events. Chloride (Cl-) concentrations in the vadose zone pore water substantially increased with depth, evidence of deep subsurface evaporation and down flushing of concentrated solutions from the evaporation zones during preferential infiltration events. These observations led to development of a Desiccation-Crack-Induced Salinization (DCIS) conceptual model. DCIS suggests that thermally driven convective air flow in the desiccation cracks induces evaporation and salinization in relatively deep sections of the subsurface. This conceptual model supports previous conceptual models on vadose zone and groundwater salinization in fractured rock in arid environments and extends its validity to clayey soils in semi-arid environments.

scholarly journals Synthetic microbial ecosystems: an exciting tool to understand and apply microbial communities

2013 ◽  
Vol 16 (6) ◽  
pp. 1472-1481 ◽  
Author(s):  
Karen De Roy ◽  
Massimo Marzorati ◽  
Pieter Van den Abbeele ◽  
Tom Van de Wiele ◽  
Nico Boon
Keyword(s):  
Microbial Communities ◽  
Microbial Ecosystems

Resilience of floodplain ecosystems in a semi-arid environment

2010 ◽  
Vol 32 (3) ◽  
pp. 305 ◽  
Author(s):  
Matthew J. Colloff ◽  
Darren S. Baldwin
Keyword(s):  
Stable State ◽  
Arid Environment ◽  
Ecosystem Functions ◽  
Arid Environments ◽  
Ecosystem Resilience ◽  
Floodplain Ecosystems ◽  
Murray Darling Basin ◽  
Single State ◽  
Floods And Droughts ◽  
Semi Arid

Implicit to loss of ecosystem resilience is that systems can shift from one stable state to another as a result of disturbance. We present a conceptual model of ecosystem resilience of floodplains and wetlands in semi-arid environments like those of the Murray–Darling Basin. The model is based on a single state characterised by fluctuating wet and dry phases driven by episodic floods and droughts. It might appear that such a single state is inherently unstable, but stability, and the measure of resilience, is conferred by the capacity of floodplains and wetlands to undergo drought and yet return to a functioning wet phase following inundation as well as to undergo flooding and return to the dry phase following flood recession. Floodplains and wetlands are driven by strong, periodic abiotic disturbances and their ecosystem functions and biogeochemical processes are highly rate-limited, spatiotemporally variable and driven by relatively species-poor assemblages of plants and animals adapted to withstand drought and flooding. Extreme drying due to climatic change and over-allocation of water resources represents the primary mechanism via which resilience is lost.

scholarly journals Desiccation-crack-induced salinization in deep clay sediment

2013 ◽  
Vol 17 (4) ◽  
pp. 1533-1545 ◽  
Author(s):  
S. Baram ◽  
Z. Ronen ◽  
D. Kurtzman ◽  
C. Külls ◽  
O. Dahan
Keyword(s):  
Isotopic Composition ◽  
Conceptual Model ◽  
Pore Water ◽  
Vadose Zone ◽  
Land Surface ◽  
Water Infiltration ◽  
Arid Environments ◽  
Desiccation Cracks ◽  
The Impact ◽  
Desiccation Crack

Abstract. A study on water infiltration and solute transport in a clayey vadose zone underlying a dairy farm waste source was conducted to assess the impact of desiccation cracks on subsurface evaporation and salinization. The study is based on five years of continuous measurements of the temporal variation in the vadose zone water content and on the chemical and isotopic composition of the sediment and pore water in it. The isotopic composition of water stable isotopes (δ18O and δ2H) in water and sediment samples, from the area where desiccation crack networks prevail, indicated subsurface evaporation down to ~ 3.5 m below land surface, and vertical and lateral preferential transport of water, following erratic preferential infiltration events. Chloride (Cl−) concentrations in the vadose zone pore water substantially increased with depth, evidence of deep subsurface evaporation and down flushing of concentrated solutions from the evaporation zones during preferential infiltration events. These observations led to development of a desiccation-crack-induced salinization (DCIS) conceptual model. DCIS suggests that thermally driven convective air flow in the desiccation cracks induces evaporation and salinization in relatively deep sections of the subsurface. This conceptual model supports previous conceptual models on vadose zone and groundwater salinization in fractured rock in arid environments and extends its validity to clayey soils in semi-arid environments.

scholarly journals Spatial heterogeneity of the shorebird gastrointestinal microbiome

2020 ◽  
Vol 7 (1) ◽  
pp. 191609
Author(s):  
Kirsten Grond ◽  
Hannah Guilani ◽  
Sarah M. Hird
Keyword(s):  
Microbial Communities ◽  
Large Intestine ◽  
Alpha Diversity ◽  
Source Tracking ◽  
Similar Species ◽  
Gastrointestinal Microbiome ◽  
Semipalmated Sandpiper ◽  
Microbial Ecosystems ◽  
Genus Richness ◽  
Intestine Microbiome

The gastrointestinal tract (GIT) consists of connected structures that vary in function and physiology, and different GIT sections potentially provide different habitats for microorganisms. Birds possess unique GIT structures, including the oesophagus, proventriculus, gizzard, small intestine, caeca and large intestine. To understand birds as hosts of microbial ecosystems, we characterized the microbial communities in six sections of the GIT of two shorebird species, the Dunlin and Semipalmated Sandpiper, identified potential host species effects on the GIT microbiome and used microbial source tracking to determine microbial origin throughout the GIT. The upper three GIT sections had higher alpha diversity and genus richness compared to the lower sections, and microbial communities in the upper GIT showed no clustering. The proventriculus and gizzard microbiomes primarily originated from upstream sections, while the majority of the large intestine microbiome originated from the caeca. The heterogeneity of the GIT sections shown in our study urges caution in equating data from faeces or a single GIT component to the entire GIT microbiome but confirms that ecologically similar species may share many attributes in GIT microbiomes.

scholarly journals Surface Roughness Estimation in the Orog Nuur Basin (Southern Mongolia) Using Sentinel-1 SAR Time Series and Ground-Based Photogrammetry

2020 ◽  
Vol 12 (19) ◽  
pp. 3200
Author(s):  
Tobias Ullmann ◽  
Georg Stauch
Keyword(s):  
Time Series ◽  
Surface Roughness ◽  
Root Mean Square ◽  
Land Surface ◽  
Arid Environment ◽  
Mean Square ◽  
Geomorphological Mapping ◽  
Multi Temporal ◽  
Dry Conditions ◽  
Single Field

This study demonstrates an application-oriented approach to estimate area-wide surface roughness from Sentinel-1 time series in the semi-arid environment of the Orog Nuur Basin (southern Mongolia) to support recent geomorphological mapping efforts. The relation of selected mono- and multi-temporal SAR features and roughness is investigated by using an empirical multi-model approach and selected 1D and 2D surface roughness indices. These indices were obtained from 48 high-resolution ground-based photogrammetric digital elevation models, which were acquired during a single field campaign. The analysis is backed by a time series analysis, comparing Sentinel-1 features to temporal-corresponding observations and reanalysis datasets on soil moisture conditions, land surface temperature, occurrence of precipitation events, and presence and development of vegetation. Results show that Sentinel-1 features are hardly sensitive to the changing surface conditions over none to sparsely vegetated land, indicating very dry conditions throughout the year. Consequently, surface roughness is the dominating factor altering SAR intensity. The best correlation is found for the combined surface roughness index Z-Value (ratio between the root mean square height and the correlation length) and the mean summer VH intensity with an r2 coefficient of 0.83 and an Root-Mean-Square Error of 0.032.

scholarly journals Google Earth Engine for the Detection of Soiling on Photovoltaic Solar Panels in Arid Environments

2020 ◽  
Vol 12 (9) ◽  
pp. 1466 ◽  
Author(s):  
Hitesh Supe ◽  
Ram Avtar ◽  
Deepak Singh ◽  
Ankita Gupta ◽  
Ali P. Yunus ◽  
...  
Keyword(s):  
Land Surface ◽  
Power Plants ◽  
Remote Sensing Data ◽  
Bare Soil ◽  
Google Earth ◽  
Landsat 8 ◽  
Arid Environments ◽  
Solar Panels ◽  
Google Earth Engine ◽  
Sand Deposition

The soiling of solar panels from dry deposition affects the overall efficiency of power output from solar power plants. This study focuses on the detection and monitoring of sand deposition (wind-blown dust) on photovoltaic (PV) solar panels in arid regions using multitemporal remote sensing data. The study area is located in Bhadla solar park of Rajasthan, India which receives numerous sandstorms every year, carried by westerly and north-westerly winds. This study aims to use Google Earth Engine (GEE) in monitoring the soiling phenomenon on PV panels. Optical imageries archived in the GEE platform were processed for the generation of various sand indices such as the normalized differential sand index (NDSI), the ratio normalized differential soil index (RNDSI), and the dry bare soil index (DBSI). Land surface temperature (LST) derived from Landsat 8 thermal bands were also used to correlate with sand indices and to observe the pattern of sand accumulation in the target region. Additionally, high-resolution PlanetScope images were used to quantitatively validate the sand indices. Our study suggests that the use of freely available satellite data with semiautomated processing on GEE can be a useful alternative to manual methods. The developed method can provide near real-time monitoring of soiling on PV panels cost-effectively. This study concludes that the DBSI method has a comparatively higher potential (89.6% Accuracy, 0.77 Kappa) in the detection of sand deposition on PV panels as compared to other indices. The findings of this study can be useful to solar energy companies in the development of an operational plan for the cleaning of PV panels regularly.

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