Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes

Thiocyanate (SCN–) contamination threatens aquatic ecosystems and pollutes vital freshwater supplies. SCN–-degrading microbial consortia are commercially adapted for remediation, but the impact of organic amendments on selection within SCN–-degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN– could be reproducibly selected for based on SCN– loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN–-contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN–-degrading consortium. Five experiments were conducted over 790 days, and genome-resolved metagenomics was used to resolve community composition at the strain level. A single Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to break down SCN– using a novel thiocyanate desulfurase, oxidize resulting reduced sulfur, degrade product cyanate to ammonia and CO2 via cyanate hydratase, and fix CO2 via the Calvin–Benson–Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Although sustained by autotrophy, reactors without molasses did not stably degrade SCN– at high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.

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Thiocyanate and organic carbon inputs drive convergent selection for specific autotrophic Afipia and Thiobacillus strains within complex microbiomes

10.1101/2020.04.29.067207 ◽

2020 ◽

Cited By ~ 1

Author(s):

Robert J. Huddy ◽

Rohan Sachdeva ◽

Fadzai Kadzinga ◽

Rose Kantor ◽

Susan T.L. Harrison ◽

...

Keyword(s):

Organic Carbon ◽

Microbial Communities ◽

Organic Amendments ◽

Microbial Consortia ◽

Contaminated Water ◽

Community Members ◽

Loading Rates ◽

Niche Diversity ◽

Selection For ◽

The Impact

AbstractThiocyanate (SCN-) contamination threatens aquatic ecosystems and pollutes vital fresh water supplies. SCN- degrading microbial consortia are commercially deployed for remediation, but the impact of organic amendments on selection within SCN- degrading microbial communities has not been investigated. Here, we tested whether specific strains capable of degrading SCN- could be reproducibly selected for based on SCN- loading and the presence or absence of added organic carbon. Complex microbial communities derived from those used to treat SCN- contaminated water were exposed to systematically increased input SCN concentrations in molasses-amended and -unamended reactors and in reactors switched to unamended conditions after establishing the active SCN- degrading consortium. Five experiments were conducted over 790 days and genome-resolved metagenomics was used to resolve community composition at the strain level. A single Thiobacillus strain proliferated in all reactors at high loadings. Despite the presence of many Rhizobiales strains, a single Afipia variant dominated the molasses-free reactor at moderately high loadings. This strain is predicted to breakdown SCN- using a novel thiocyanate dehydrogenase, oxidize resulting reduced sulfur, degrade product cyanate (OCN−) to ammonia and CO2 via cyanase, and fix CO2 via the Calvin-Benson-Bassham cycle. Removal of molasses from input feed solutions reproducibly led to dominance of this strain. Neither this Afipia strain nor the thiobacilli have the capacity to produce cobalamin, a function detected in low abundance community members. Although sustained by autotrophy, reactors without molasses did not stably degrade SCN- at high loading rates, perhaps due to loss of biofilm-associated niche diversity. Overall, convergence in environmental conditions led to convergence in the strain composition, although reactor history also impacted the trajectory of community compositional change.

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Livestock as vectors of organic matter and nutrient loading in aquatic ecosystems in African savannas

PLoS ONE ◽

10.1371/journal.pone.0257076 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257076

Author(s):

Jacob O. Iteba ◽

Thomas Hein ◽

Gabriel A. Singer ◽

Frank O. Masese

Keyword(s):

Organic Matter ◽

Organic Carbon ◽

Aquatic Ecosystems ◽

Dry Matter ◽

Nutrient Loading ◽

Nutrient Transport ◽

Zebu Cattle ◽

Loading Rates ◽

The World ◽

Direct Input

Populations of large wildlife have declined in many landscapes around the world, and have been replaced or displaced by livestock. The consequences of these changes on the transfer of organic matter (OM) and nutrients from terrestrial to aquatic ecosystems are not well understood. We used behavioural data, excretion and egestion rates and C: N: P stoichiometry of dung and urine of zebu cattle, to develop a metabolism-based estimate of loading rates of OM (dung), C, N and P into the Mara River, Kenya. We also directly measured the deposition of OM and urine by cattle into the river during watering. Per head, zebu cattle excrete and/or egest 25.6 g dry matter (DM, 99.6 g wet mass; metabolism) - 27.7 g DM (direct input) of OM, 16.0–21.8 g C, 5.9–9.6 g N, and 0.3–0.5 g P per day into the river. To replace loading rates OM of an individual hippopotamus by cattle, around 100 individuals will be needed, but much less for different elements. In parts of the investigated sub-catchments loading rates by cattle were equivalent to or higher than that of the hippopotamus. The patterns of increased suspended materials and nutrients as a result of livestock activity fit into historical findings on nutrients concentrations, dissolved organic carbon and other variables in agricultural and livestock areas in the Mara River basin. Changing these patterns of carbon and nutrient transport and cycling are having significant effects on the structure and functioning of both terrestrial and aquatic ecosystems.

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Microbiome Composition and Function in Aquatic Vertebrates: Small Organisms Making Big Impacts on Aquatic Animal Health

Frontiers in Microbiology ◽

10.3389/fmicb.2021.567408 ◽

2021 ◽

Vol 12 ◽

Author(s):

Ludek Sehnal ◽

Elizabeth Brammer-Robbins ◽

Alexis M. Wormington ◽

Ludek Blaha ◽

Joe Bisesi ◽

...

Keyword(s):

Microbial Communities ◽

Aquatic Ecosystems ◽

Marine Mammals ◽

Integrative Approach ◽

Aquatic Animal ◽

Gastrointestinal Microbiota ◽

Microbial Composition ◽

Aquatic Vertebrates ◽

And Function ◽

The Impact

Aquatic ecosystems are under increasing stress from global anthropogenic and natural changes, including climate change, eutrophication, ocean acidification, and pollution. In this critical review, we synthesize research on the microbiota of aquatic vertebrates and discuss the impact of emerging stressors on aquatic microbial communities using two case studies, that of toxic cyanobacteria and microplastics. Most studies to date are focused on host-associated microbiomes of individual organisms, however, few studies take an integrative approach to examine aquatic vertebrate microbiomes by considering both host-associated and free-living microbiota within an ecosystem. We highlight what is known about microbiota in aquatic ecosystems, with a focus on the interface between water, fish, and marine mammals. Though microbiomes in water vary with geography, temperature, depth, and other factors, core microbial functions such as primary production, nitrogen cycling, and nutrient metabolism are often conserved across aquatic environments. We outline knowledge on the composition and function of tissue-specific microbiomes in fish and marine mammals and discuss the environmental factors influencing their structure. The microbiota of aquatic mammals and fish are highly unique to species and a delicate balance between respiratory, skin, and gastrointestinal microbiota exists within the host. In aquatic vertebrates, water conditions and ecological niche are driving factors behind microbial composition and function. We also generate a comprehensive catalog of marine mammal and fish microbial genera, revealing commonalities in composition and function among aquatic species, and discuss the potential use of microbiomes as indicators of health and ecological status of aquatic ecosystems. We also discuss the importance of a focus on the functional relevance of microbial communities in relation to organism physiology and their ability to overcome stressors related to global change. Understanding the dynamic relationship between aquatic microbiota and the animals they colonize is critical for monitoring water quality and population health.

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Responses of Soil Organic Carbon Mineralization and Microbial Communities to Leaf Litter Addition under Different Soil Layers

Forests ◽

10.3390/f12020170 ◽

2021 ◽

Vol 12 (2) ◽

pp. 170

Author(s):

Min Zhang ◽

Li-Guo Dong ◽

Shi-Xuan Fei ◽

Jia-Wen Zhang ◽

Xu-Meng Jiang ◽

...

Keyword(s):

Organic Carbon ◽

Soil Organic Carbon ◽

Microbial Communities ◽

Soil Carbon ◽

C:N Ratio ◽

Carbon Mineralization ◽

Deep Soil ◽

Soil Organic Carbon Mineralization ◽

Organic Carbon Mineralization ◽

The Impact

The mechanism of how soil carbon pools change when coniferous forests are converted into conifer-broadleaf mixed forests is poorly understood. In this study, the impact of additional carbon inputs on soil organic carbon mineralization and microbial communities was evaluated. In a microcosm incubation experiment, three types of 13C-labeled litter (Pinustabulaeformis (PT), Robiniapseudoacacia (RP), and a mixture of PT and RP (1:1, PR)) were added in to top (0–20 cm) and deep (60–80 cm) soil collected from a Chinese pine plantation. The priming effect (PE) and specific microbial groups involved in PE were studied. PT and RP addition to topsoil induced a negative PE. In deep soil, the decomposition rates of soil organic matter (SOM) after adding PT and mixture increased by 16.6% and 34.6% compared to those without litter. The addition of RP with a lower C:N ratio had a stronger negative PE than adding PT or mixture. Moreover, the PE in deep soil was more intense after all litter additions. In topsoil, the litter-derived carbon was mainly incorporated into 16:0, 18:1ω9c, and 18:1ω7c fatty acids. In conclusion, the addition of broadleaf litter into coniferous plantations might be beneficial for enhancing deep soil carbon stocks.

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Livestock as vectors of organic matter and nutrient loading in aquatic ecosystems in African savannas

10.1101/2021.07.13.452213 ◽

2021 ◽

Author(s):

Jacob O. Iteba ◽

Thomas Hein ◽

Gabriel Singer ◽

Frank O Masese

Keyword(s):

Organic Matter ◽

Organic Carbon ◽

Dissolved Organic Carbon ◽

Aquatic Ecosystems ◽

Dry Matter ◽

Nutrient Loading ◽

Zebu Cattle ◽

Loading Rates ◽

The World ◽

Direct Input

Populations of large wildlife have declined in many landscapes around the world, and have been replaced or displaced by livestock. The consequences of these changes on the transfer of organic matter (OM) and nutrients from terrestrial to aquatic ecosystems are not well understood. We used behavioural data, excretion and egestion rates and C: N: P stoichiometry of dung and urine of zebu cattle, to develop a metabolism-based estimate of loading rates of OM (dung), C, N and P into the Mara River, Kenya. We also directly measured the deposition of OM and urine by cattle into the river during watering. Per head, zebu cattle excrete and/or egest 25.6 g dry matter (DM, 99.6 g wet mass; metabolism) - 27.7 g DM (direct input) of OM, 16.0-21.8 g C, 5.9-9.6 g N, and 0.3-0.5 g P per day into the river. To replace loading rates OM of an individual hippopotamus by cattle, around 100 individuals will be needed, but much less for different elements. In parts of the investigated sub-catchments loading rates by cattle were equivalent to or higher than that of the hippopotamus. The patterns of increased suspended materials and nutrients as a result of livestock activity fit into historical findings on nutrients concentrations, dissolved organic carbon and other variables in agricultural and livestock areas in the Mara River basin. Changing these patterns of OM and nutrients transport and cycling are having significant effects on the structure and functioning of both terrestrial and aquatic ecosystems.

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Stabilization of Organic Carbon and Nitrogen in Consolidating Benthal Deposits

Water Science & Technology ◽

10.2166/wst.1985.0191 ◽

1985 ◽

Vol 17 (6-7) ◽

pp. 929-940 ◽

Cited By ~ 1

Author(s):

C. W. Bryant ◽

L. G. Rich

Keyword(s):

Organic Carbon ◽

Model Verification ◽

Volatile Acid ◽

Free Energies ◽

Organic Loading ◽

Carbon And Nitrogen ◽

Loading Rates ◽

Degradation Reactions ◽

The Individual ◽

Organic Deposits

The objective of this research was to develop and validate a predictive model of the benthal stabilization of organic carbon and nitrogen in deposits of waste activated sludge solids formed at the bottom of an aerated water column, under conditions of continual deposition. A benthal model was developed from a one-dimensional, generalized transport equation and a set of first-order biological reactions. For model verification, depth profiles of the major interstitial carbon and nitrogen components were measured from a set of deposits formed in the laboratory at 20°C and a controlled loading rate. The observed sequence of volatile acid utilization in each benthal deposit was that which would be predicted by the Gibbs free energies of the individual degradation reactions and would be controlled by the reduction in interstitial hydrogen partial pressure with time. Biodegradable solids were solubilized rapidly during the first three weeks of benthal retention, but subsequent solubilization occurred much more slowly. The benthal simulation effectively predicted the dynamics of consolidating, organic deposits. Simulation of organic loading rates up to 250 g BVSS/(m2 day) indicated that the stabilization capacity of benthal deposits was far above the range of organic loading rates currently used in lagoon design.

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Chemical Transport Facilitated by Multiphase Flow Systems1

Water Science & Technology ◽

10.2166/wst.1985.0078 ◽

1985 ◽

Vol 17 (9) ◽

pp. 1-12 ◽

Cited By ~ 11

Author(s):

Carl G. Enfield

Keyword(s):

Organic Carbon ◽

Boundary Conditions ◽

Transport Equation ◽

Fluid Phase ◽

Chemical Transport ◽

Facilitated Transport ◽

Organic Fraction ◽

Dispersive Transport ◽

Transformation Of Variables ◽

The Impact

Relatively immobile chemicals have been observed moving significantly faster than anticipated from hydrophobic theory. A theory is developed considering transport in three mobile fluid phases which can be used to describe this facilitated transport. The convective dispersive transport equation is solved utilizing a transformation of variables which permits utilizing existing solutions covering a wide variety of boundary conditions. The impact of the facilitated transport is demonstrated for one case where the soils organic carbon is 10%. If 2% of the fluid phase is an organic fraction, the theory developed projects that hydrophobic theory may underestimate mobility by more than 100 times. At concentrations of dissolved organic carbon normally observed in nature (5 - 10 mg/l), a measurable increased mobility is anticipated for the very immobile compounds like dioxins.

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From the Ground Up: Prairies on Reclaimed Mine Land—Impacts on Soil and Vegetation

Land ◽

10.3390/land9110455 ◽

2020 ◽

Vol 9 (11) ◽

pp. 455

Author(s):

Rebecca M. Swab ◽

Nicola Lorenz ◽

Nathan R. Lee ◽

Steven W. Culman ◽

Richard P. Dick

Keyword(s):

Organic Carbon ◽

Soil Organic Carbon ◽

Soil Properties ◽

Plant Community ◽

Prairie Restoration ◽

Native Plant ◽

Soil Microbial ◽

Prairie Restorations ◽

Mine Lands ◽

The Impact

After strip mining, soils typically suffer from compaction, low nutrient availability, loss of soil organic carbon, and a compromised soil microbial community. Prairie restorations can improve ecosystem services on former agricultural lands, but prairie restorations on mine lands are relatively under-studied. This study investigated the impact of prairie restoration on mine lands, focusing on the plant community and soil properties. In southeast Ohio, 305 ha within a ~2000 ha area of former mine land was converted to native prairie through herbicide and planting between 1999–2016. Soil and vegetation sampling occurred from 2016–2018. Plant community composition shifted with prairie age, with highest native cover in the oldest prairie areas. Prairie plants were more abundant in older prairies. The oldest prairies had significantly more soil fungal biomass and higher soil microbial biomass. However, many soil properties (e.g., soil nutrients, β-glucosoidase activity, and soil organic carbon), as well as plant species diversity and richness trended higher in prairies, but were not significantly different from baseline cool-season grasslands. Overall, restoration with prairie plant communities slowly shifted soil properties, but mining disturbance was still the most significant driver in controlling soil properties. Prairie restoration on reclaimed mine land was effective in establishing a native plant community, with the associated ecosystem benefits.

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Organic mulching promotes soil organic carbon accumulation to deep soil layer in an urban plantation forest

Forest Ecosystems ◽

10.1186/s40663-020-00278-5 ◽

2021 ◽

Vol 8 (1) ◽

Author(s):

Xiaodan Sun ◽

Gang Wang ◽

Qingxu Ma ◽

Jiahui Liao ◽

Dong Wang ◽

...

Keyword(s):

Organic Carbon ◽

Soil Organic Carbon ◽

Carbon Content ◽

Fine Roots ◽

Soil Layer ◽

Carbon Accumulation ◽

Bulk Soil ◽

Organic Mulch ◽

The Impact ◽

Soc Fractions

Abstract Background Soil organic carbon (SOC) is important for soil quality and fertility in forest ecosystems. Labile SOC fractions are sensitive to environmental changes, which reflect the impact of short-term internal and external management measures on the soil carbon pool. Organic mulching (OM) alters the soil environment and promotes plant growth. However, little is known about the responses of SOC fractions in rhizosphere or bulk soil to OM in urban forests and its correlation with carbon composition in plants. Methods A one-year field experiment with four treatments (OM at 0, 5, 10, and 20 cm thicknesses) was conducted in a 15-year-old Ligustrum lucidum plantation. Changes in the SOC fractions in the rhizosphere and bulk soil; the carbon content in the plant fine roots, leaves, and organic mulch; and several soil physicochemical properties were measured. The relationships between SOC fractions and the measured variables were analysed. Results The OM treatments had no significant effect on the SOC fractions, except for the dissolved organic carbon (DOC). OM promoted the movement of SOC to deeper soil because of the increased carbon content in fine roots of subsoil. There were significant correlations between DOC and microbial biomass carbon and SOC and easily oxidised organic carbon. The OM had a greater effect on organic carbon fractions in the bulk soil than in the rhizosphere. The thinnest (5 cm) mulching layers showed the most rapid carbon decomposition over time. The time after OM had the greatest effect on the SOC fractions, followed by soil layer. Conclusions The frequent addition of small amounts of organic mulch increased SOC accumulation in the present study. OM is a potential management model to enhance soil organic matter storage for maintaining urban forest productivity.

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Site-Specific Effects of Organic Amendments on Parameters of Tropical Agricultural Soil and Yield: A Field Experiment in Three Countries in Southeast Asia

Agronomy ◽

10.3390/agronomy11020348 ◽

2021 ◽

Vol 11 (2) ◽

pp. 348

Author(s):

Thuy Thu Doan ◽

Phimmasone Sisouvanh ◽

Thanyakan Sengkhrua ◽

Supranee Sritumboon ◽

Cornelia Rumpel ◽

...

Keyword(s):

Organic Carbon ◽

Southeast Asia ◽

Biomass Production ◽

Nutrient Availability ◽

Organic Amendments ◽

Water Infiltration ◽

Elemental Content ◽

Soil Parameters ◽

Short Term ◽

Site Specific

Organic amendments may improve the quality of acidic tropical agricultural soils with low organic carbon contents under conventional management (mineral fertilization and irrigation) in Southeast Asia. We investigated the effect of biochar, compost and their combination on maize growth and yield, soil physical, biological and chemical properties at harvesting time at four sites in three countries: Thailand, Vietnam and Laos. Treatments consisted of 10 t·ha−1 cow manure compost and 7 t·ha−1 of Bamboo biochar and their combination. Maize biomass production and cop yields were recorded for two seasons. Elemental content, pH and nutrient availability of soils were analyzed after the first growing season. We also characterized macrofauna abundance and water infiltration. Few changes were noted for maize biomass production and maize cop yield. Soil chemical parameters showed contrasting, site-specific results. Compost and biochar amendments increased soil organic carbon, pH, total K and N, P and K availability especially for sandy soils in Thailand. The combination of both amendments could reduce nutrient availability as compared to compost only treatments. Physical and biological parameters showed no treatment response. We conclude that the addition of compost, biochar and their mixture to tropical soils have site-specific short-term effects on chemical soil parameters. Their short-term effect on plants is thus mainly related to nutrient input. The site-dependent results despite similar crops, fertilization and irrigation practices suggest that inherent soil parameters and optimization of organic amendment application to specific pedoclimatic conditions need future attention.

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