Salinity Drives Functional and Taxonomic Diversities in Global Water Metagenomes

A tight association between microbial function and taxonomy is the basis of functional prediction based on taxonomy, but such associations have been controversial in water biomes largely due to the probable prevalence of functional redundancy. However, previous studies on this topic used a relatively coarse resolution of ecosystem functioning, potentially inflating the estimated functional redundancy. Thus, a comprehensive evaluation of the association between high-resolution functional traits and taxonomic diversity obtained from fresh and saline water metagenomic data is urgently needed. Here, we examined 938 functionally and taxonomically annotated water metagenomes obtained worldwide to scrutinize the connection between function and taxonomy, and to identify the key driver of water metagenomes function or taxonomic composition at a global scale. We found that pairwise similarity of function was significantly associated with taxonomy, though taxonomy had higher global dissimilarity than function. Classification into six water biomes resulted in greater variation in taxonomic compositions than functional profiles, as the key regulating factor was salinity. Fresh water microbes harbored distinct functional and taxonomic structures from microbes in saline water biomes, despite that taxonomy was more susceptible to gradient of geography and climate than function. In summary, our results find a significant relationship between taxonomic diversity and microbial functioning in global water metagenomes, although microbial taxonomic compositions vary to a larger extent than functional profiles in aquatic ecosystems, suggesting the possibility and necessity for functional prediction of microorganisms based on taxonomy in global aquatic ecosystems.

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Lower functional redundancy in “narrow” than “broad” functions in global soil metagenomics

10.5194/soil-2021-148 ◽

2022 ◽

Author(s):

Huaihai Chen ◽

Kayan Ma ◽

Yu Huang ◽

Jiajiang Lin ◽

Christopher Schadt ◽

...

Keyword(s):

Functional Diversity ◽

Soil Microbes ◽

Taxonomic Diversity ◽

Functional Redundancy ◽

Ecosystem Functions ◽

Soil Microbial ◽

Wide Range ◽

Global Soil ◽

Functional Profiles ◽

The Relationship

Abstract. Understanding the relationship between soil microbial taxonomic compositions and functional profiles is essential for predicting ecosystem functions under various environmental disturbances. However, even though microbial communities are sensitive to disturbance, ecosystem functions remain relatively stable, as soil microbes are likely to be functionally redundant. Microbial functional redundancy may be more associated with “broad” functions carried out by a wide range of microbes, than with “narrow” functions specialized by specific microorganisms. Thus, a comprehensive study to evaluate how microbial taxonomic compositions correlate with “broad” and “narrow” functional profiles is necessary. Here, we evaluated soil metagenomes worldwide to assess whether functional and taxonomic diversities differ significantly between the five “broad” and the five “narrow” functions that we chose. Our results revealed that compared with the five “broad” functions, soil microbes capable of performing the five “narrow” functions were more taxonomically diverse, and thus their functional diversity was more dependent on taxonomic diversity, implying lower levels of functional redundancy in “narrow” functions. Co-occurrence networks indicated that microorganisms conducting “broad” functions were positively related, but microbes specializing “narrow” functions were interacting mostly negatively. Our study provides strong evidence to support our hypothesis that functional redundancy is significantly different between “broad” and “narrow” functions in soil microbes, as the association of functional diversity with taxonomy were greater in the five “narrow” rather than the five “broad” functions.

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Groundwater phosphorus concentrations: global trends and links with agricultural and oil and gas activities

10.5194/egusphere-egu21-12260 ◽

2021 ◽

Author(s):

Jessica Warrack ◽

Mary Kang ◽

Christian von Sperber

Keyword(s):

Oil And Gas ◽

Comprehensive Evaluation ◽

Significant Risk ◽

Surface Water Quality ◽

The United States ◽

Global Scale ◽

Anthropogenic Sources ◽

High Concentration ◽

Oil And Gas Development ◽

Global Trends

<p>Although observations show that anthropogenic phosphorus (P) can reach groundwater supplies, there has been no comprehensive evaluation of P in groundwater at the global scale. Additionally, there have been minimal studies on distributed sources, such as agriculture, and the effects of oil and gas activities on P contamination in groundwater are poorly understood. We compile and analyze 181,653 groundwater P concentrations from 13 government agencies and 8 individual research studies in 11 different countries in order to determine the extent of P pollution at the global scale. We find that every country with data has groundwater P concentrations that pose a significant risk of eutrophication to surface waters. In Canada and the United States, we study the relationship between land use, focusing on crop/pastureland, and increased P concentrations in groundwater. In Ontario and Alberta, two Canadian provinces with different histories of oil and gas development, we find areas with a high concentration of P groundwater pollution to coincide with regions of intense oil and gas activity. Understanding the effects of anthropogenic sources on phosphorus contamination of groundwater and identifying all possible pathways through which contamination can occur will assist regulators in planning and implementing effective strategies to manage groundwater and surface water quality and sustain ecosystem health.</p>

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A Comparative Analysis of Biosynthetic Gene Clusters in Lean and Obese Humans

BioMed Research International ◽

10.1155/2019/6361320 ◽

2019 ◽

Vol 2019 ◽

pp. 1-7 ◽

Cited By ~ 1

Author(s):

Shengqin Wang ◽

Na Li ◽

Nan Li ◽

Huixi Zou ◽

Mingjiang Wu

Keyword(s):

Gut Microbiome ◽

Gene Clusters ◽

Human Adipose Tissue ◽

Taxonomic Diversity ◽

Metagenomic Data ◽

Biosynthetic Gene ◽

Biosynthetic Gene Clusters ◽

Intestinal Microbes ◽

Microbe Interactions ◽

Treatment Of Obesity

Obesity is intrinsically linked with the gut microbiome, and studies have identified several obesity-associated microbes. The microbe-microbe interactions can alter the composition of the microbial community and influence host health by producing secondary metabolites (SMs). However, the contribution of these SMs in the prevention and treatment of obesity has been largely ignored. We identified several SM-encoding biosynthetic gene clusters (BGCs) from the metagenomic data of lean and obese individuals and found significant association between some BGCs, including those that produce hitherto unknown SM, and obesity. In addition, the mean abundance of BGCs was positively correlated with obesity, consistent with the lower taxonomic diversity in the gut microbiota of obese individuals. By comparing the BGCs of known SM between obese and nonobese samples, we found that menaquinone produced by Enterobacter cloacae showed the highest correlation with BMI, in agreement with a recent study on human adipose tissue composition. Furthermore, an obesity-related nonribosomal peptide synthetase (NRPS) was negatively associated with Bacteroidetes, indicating that the SMs produced by intestinal microbes in obese individuals can change the microbiome structure. This is the first systemic study of the association between gut microbiome BGCs and obesity and provides new insights into the causes of obesity.

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Salinisation and prospects for biodiversity in rivers and wetlands of south-west Western Australia

Australian Journal of Botany ◽

10.1071/bt02113 ◽

2003 ◽

Vol 51 (6) ◽

pp. 673 ◽

Cited By ~ 83

Author(s):

S. A. Halse ◽

J. K. Ruprecht ◽

A. M. Pinder

Keyword(s):

Western Australia ◽

Aquatic Ecosystems ◽

Saline Water ◽

Biological Communities ◽

Invertebrate Species ◽

South West ◽

Large Numbers ◽

High Concentrations ◽

Water Volumes ◽

Western Australian

Saline water was common in south-west Western Australian aquatic systems prior to land-clearing because most streams and wetlands were ephemeral and evapo-concentrated as they dried, and there were high concentrations of stored salt in groundwater and soil profiles. Nevertheless, a 1998 review of salinity trends in rivers of south-west Western Australia showed that 20-fold increases in salinity concentrations had occurred since clearing in the medium-rainfall zone (300–700 mm). More recent data confirm these trends and show that elevated salinities have already caused substantial changes to the biological communities of aquatic ecosystems. Further substantial changes will occur, despite the flora and fauna of the south-west being comparatively well adapted to the presence of salinity in the landscape. Up to one-third of wetland and river invertebrate species, large numbers of plants and a substantial proportion of the waterbird fauna will disappear from the wheatbelt, a region that has high biodiversity value and endemism. Increased salinities are not the only threat associated with salinisation: increased water volumes, longer periods of inundation and more widespread acidity are also likely to be detrimental to the biota.

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A framework to regionalize conceptual model parameters for global hydrological modeling

10.5194/hess-2020-127 ◽

2020 ◽

Author(s):

Wenyan Qi ◽

Jie Chen ◽

Lu Li ◽

Chong-yu Xu ◽

Jingjing Li ◽

...

Keyword(s):

Water Resources ◽

Conceptual Model ◽

Hydrological Modeling ◽

Global Scale ◽

Spatial Proximity ◽

Model Parameters ◽

Hydrological Models ◽

Physical Similarity ◽

Similarity Method ◽

Global Water

Abstract. To provide an accurate estimate of global water resources and help to formulate water allocation policies, global hydrological models (GHMs) have been developed. However, it is difficult to obtain parameter values for GHMs, which results in large uncertainty in estimation of the global water balance components. In this study, a framework is developed for building GHMs based on parameter regionalization of catchment scale conceptual hydrological models. That is, using appropriate global scale regionalization scheme (GSRS) and conceptual hydrological models to simulate runoff at the grid scale globally and the Network Response Routing (NRF) method to converge the grid runoff to catchment streamflow. To achieve this, five regionalization methods (i.e. the global mean method, the spatial proximity method, the physical similarity method, the physical similarity method considering distance, and the regression method) are first tested for four conceptual hydrological models over thousands medium-sized catchments (2500–50000 km2) around the world to find the appropriate global scale regionalization scheme. The selected GSRS is then used to regionalize conceptual model parameters for global land grids with 0.5°×0.5° resolution on latitude and longitude. The results show that: (1) Spatial proximity method with the Inverse Distance Weighting (IDW) method and the output average option (SPI-OUT) offers the best regionalization solution, and the greatest gains of the SPI-OUT method were achieved with mean distance between the donor catchments and the target catchment is no more than 1500 km. (2) It was found the Kling-Gupta efficiency (KGE) value of 0.5 is a good threshold value to select donor catchments. And (3) Four different GHMs established based on framework were able to produce reliable streamflow simulations. Overall, the proposal framework can be used with any conceptual hydrological model for estimating global water resources, even though uncertainty exists in terms of using difference conceptual models.

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The Global Water Body Layer from TanDEM-X Interferometric SAR Data

Remote Sensing ◽

10.3390/rs13245069 ◽

2021 ◽

Vol 13 (24) ◽

pp. 5069

Author(s):

Jose-Luis Bueso-Bello ◽

Michele Martone ◽

Carolina González ◽

Francescopaolo Sica ◽

Paolo Valdo ◽

...

Keyword(s):

Water Body ◽

European Space Agency ◽

Water Layer ◽

Global Scale ◽

Data Set ◽

Primary Input ◽

Water Detection ◽

Space Agency ◽

Digital Elevation ◽

Global Water

The interferometric synthetic aperture radar (InSAR) data set, acquired by the TanDEM-X (TerraSAR-X add-on for Digital Elevation Measurement) mission (TDM), represents a unique data source to derive geo-information products at a global scale. The complete Earth’s landmasses have been surveyed at least twice during the mission bistatic operation, which started at the end of 2010. Examples of the delivered global products are the TanDEM-X digital elevation model (DEM) (at a final independent posting of 12 m × 12 m) or the TanDEM-X global Forest/Non-Forest (FNF) map. The need for a reliable water product from TanDEM-X data was dictated by the limited accuracy and difficulty of use of the TDX Water Indication Mask (WAM), delivered as by-product of the global DEM, which jeopardizes its use for scientific applications, as well. Similarly as it has been done for the generation of the FNF map; in this work, we utilize the global data set of TanDEM-X quicklook images at 50 m × 50 m resolution, acquired between 2011 and 2016, to derive a new global water body layer (WBL), covering a range from −60∘ to +90∘ latitudes. The bistatic interferometric coherence is used as the primary input feature for performing water detection. We classify water surfaces in single TanDEM-X images, by considering the system’s geometric configuration and exploiting a watershed-based segmentation algorithm. Subsequently, single overlapping acquisitions are mosaicked together in a two-step logically weighting process to derive the global TDM WBL product, which comprises a binary averaged water/non-water layer as well as a permanent/temporary water indication layer. The accuracy of the new TDM WBL has been assessed over Europe, through a comparison with the Copernicus water and wetness layer, provided by the European Space Agency (ESA), at a 20 m × 20 m resolution. The F-score ranges from 83%, when considering all geocells (of 1∘ latitudes × 1∘ longitudes) over Europe, up to 93%, when considering only the geocells with a water content higher than 1%. At global scale, the quality of the product has been evaluated, by intercomparison, with other existing global water maps, resulting in an overall agreement that often exceeds 85% (F-score) when the content in the geocell is higher than 1%. The global TDM WBL presented in this study will be made available to the scientific community for free download and usage.

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Evaluating Stream Restoration Projects: What Do We Learn from Monitoring?

Water ◽

10.3390/w9030174 ◽

2017 ◽

Vol 9 (3) ◽

pp. 174 ◽

Cited By ~ 23

Author(s):

Zan Rubin ◽

G. Kondolf ◽

Blanca Rios-Touma

Keyword(s):

Habitat Heterogeneity ◽

Stream Restoration ◽

Habitat Restoration ◽

Taxonomic Diversity ◽

Global Scale ◽

Ecological Condition ◽

Ecosystem Change ◽

Know How ◽

Abundance And Diversity ◽

Meta Analyses

Two decades since calls for stream restoration projects to be scientifically assessed, most projects are still unevaluated, and conducted evaluations yield ambiguous results. Even after these decades of investigation, do we know how to define and measure success? We systematically reviewed 26 studies of stream restoration projects that used macroinvertebrate indicators to assess the success of habitat heterogeneity restoration projects. All 26 studies were previously included in two meta-analyses that sought to assess whether restoration programs were succeeding. By contrast, our review focuses on the evaluations themselves, and asks what exactly we are measuring and learning from these evaluations. All 26 studies used taxonomic diversity, richness, or abundance of invertebrates as biological measures of success, but none presented explicit arguments why those metrics were relevant measures of success for the restoration projects. Although changes in biodiversity may reflect overall ecological condition at the regional or global scale, in the context of reach-scale habitat restoration, more abundance and diversity may not necessarily be better. While all 26 studies sought to evaluate the biotic response to habitat heterogeneity enhancement projects, about half of the studies (46%) explicitly measured habitat alteration, and 31% used visual estimates of grain size or subjectively judged ‘habitat quality’ from protocols ill-suited for the purpose. Although the goal of all 26 projects was to increase habitat heterogeneity, 31% of the studies either sampled only riffles or did not specify the habitats sampled. One-third of the studies (35%) used reference ecosystems to define target conditions. After 20 years of stream restoration evaluation, more work remains for the restoration community to identify appropriate measures of success and to coordinate monitoring so that evaluations are at a scale capable of detecting ecosystem change.

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The Water Footprint of the United States

Water ◽

10.3390/w12113286 ◽

2020 ◽

Vol 12 (11) ◽

pp. 3286

Author(s):

Megan Konar ◽

Landon Marston

Keyword(s):

United States ◽

Water Footprint ◽

Virtual Water ◽

The United States ◽

Global Scale ◽

Future Research ◽

Special Issue ◽

Water Flows ◽

Global Water

This paper commemorates the influence of Arjen Y. Hoekstra on water footprint research of the United States. It is part of the Special Issue “In Memory of Prof. Arjen Y. Hoekstra”. Arjen Y. Hoekstra both inspired and enabled a community of scholars to work on understanding the water footprint of the United States. He did this by comprehensively establishing the terminology and methodology that serves as the foundation for water footprint research. His work on the water footprint of humanity at the global scale highlighted the key role of a few nations in the global water footprint of production, consumption, and virtual water trade. This research inspired water scholars to focus on the United States by highlighting its key role amongst world nations. Importantly, he enabled the research of many others by making water footprint estimates freely available. We review the state of the literature on water footprints of the United States, including its water footprint of production, consumption, and virtual water flows. Additionally, we highlight metrics that have been developed to assess the vulnerability, resiliency, sustainability, and equity of sub-national water footprints and domestic virtual water flows. We highlight opportunities for future research.

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Assessing Evapotranspiration Estimates from the Second Global Soil Wetness Project (GSWP-2) Simulations

Journal of Hydrometeorology ◽

10.1175/2010jhm1203.1 ◽

2010 ◽

Vol 11 (4) ◽

pp. 880-897 ◽

Cited By ~ 22

Author(s):

C. Adam Schlosser ◽

Xiang Gao

Keyword(s):

High Latitude ◽

Land Surface ◽

Water Budget ◽

Global Scale ◽

Atmospheric Forcing ◽

Global Land ◽

Global Soil ◽

Soil Wetness ◽

Annual Water ◽

Global Water

Abstract This study assesses the simulations of global-scale evapotranspiration from the second Global Soil Wetness Project (GSWP-2) within a global water budget framework. The scatter in the GSWP-2 global evapotranspiration estimates from various land surface models can constrain the global annual water budget fluxes to within ±2.5% and, by using estimates of global precipitation, the residual ocean evaporation estimate falls within the range of other independently derived bulk estimates. The GSWP-2 scatter, however, cannot entirely explain the imbalance of the annual fluxes from a modern-era, observationally based global water budget assessment. Inconsistencies in the magnitude and timing of seasonal variations between the global water budget terms are also found. Intermodel inconsistencies in evapotranspiration are largest for high-latitude interannual variability as well as for interseasonal variations in the tropics, and analyses with field-scale data also highlight model disparity at estimating evapotranspiration in high-latitude regions. Analyses of the sensitivity simulations that replace uncertain forcings (i.e., radiation, precipitation, and meteorological variables) indicate that global (land) evapotranspiration is slightly more sensitive to precipitation than net radiation perturbations, and the majority of the GSWP-2 models, at a global scale, fall in a marginally moisture-limited evaporative condition. Lastly, the range of global evapotranspiration estimates among the models is larger than any bias caused by uncertainties in the GSWP-2 atmospheric forcing, indicating that model structure plays a more important role toward improving global land evaporation estimates (as opposed to improved atmospheric forcing).

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The kinetoplastid-infecting Bodo saltans virus (BsV), a window into the most abundant giant viruses in the sea

eLife ◽

10.7554/elife.33014 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 37

Author(s):

Christoph M Deeg ◽

Cheryl-Emiliane T Chow ◽

Curtis A Suttle

Keyword(s):

Aquatic Ecosystems ◽

Homing Endonuclease ◽

Rapid Evolution ◽

Host Factors ◽

Metagenomic Data ◽

Replication Machinery ◽

Genomic Plasticity ◽

Giant Viruses ◽

Translational Apparatus ◽

Self Splicing

Giant viruses are ecologically important players in aquatic ecosystems that have challenged concepts of what constitutes a virus. Herein, we present the giant Bodo saltans virus (BsV), the first characterized representative of the most abundant group of giant viruses in ocean metagenomes, and the first isolate of a klosneuvirus, a subgroup of the Mimiviridae proposed from metagenomic data. BsV infects an ecologically important microzooplankton, the kinetoplastid Bodo saltans. Its 1.39 Mb genome encodes 1227 predicted ORFs, including a complex replication machinery. Yet, much of its translational apparatus has been lost, including all tRNAs. Essential genes are invaded by homing endonuclease-encoding self-splicing introns that may defend against competing viruses. Putative anti-host factors show extensive gene duplication via a genomic accordion indicating an ongoing evolutionary arms race and highlighting the rapid evolution and genomic plasticity that has led to genome gigantism and the enigma that is giant viruses.

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