Fitorremediación asistida a través de bacterias, para suelos contaminados con metales pesados y plaguicidas

TANIA GÓMEZ MORALES (2023, [Otro, Trabajo terminal, especialidad])

El suelo es un recurso no renovable que nos proporciona diferentes beneficios, incluidos los servicios ecosistémicos. Sin embargo, actividades antropogénicas como la minería y la agricultura lo han contaminado. Las prácticas mineras y agrícolas liberan contaminantes como plaguicidas y metales pesados al suelo como contaminantes individuales o mezclas, generando importantes efectos adversos para el ambiente y la salud humana. Debido a esta problemática, se han desarrollado diferentes estrategias de remediación para sitios con presencia de estos co-contaminantes. Una de ellas es la fitorremediación asistida por bacterias, una técnica basada en la asociación de plantas y bacterias, donde ambos organismos se benefician y mejoran la eficiencia de la remediación.

Soil is a non-renewable resource that provides us with different benefits, including ecosystem services. However, anthropogenic activities such as mining and agriculture have contaminated it. Minery and agriculture practices release contaminants such as pesticides and heavy metals into the soil as individual pollutants or mixtures, generating important adverse environmental and human health effects. Due to this problem, different remediation strategies have been developed for sites with the presence of these co-contaminants; one of them is bacterial-assisted phytoremediation, a technique based on the association of plants and bacteria, where both organisms benefit and improve remediation efficiency.

BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA suelo, fitorremediación, bacterias, plaguicidas, metales pesados, co-contaminados. soil, phytoremediation, bacteria, pesticides, heavy metals, co-contaminated

DINÁMICA DE ACUMULACIÓN DE ARSÉNICO EN RELACIÓN A OTROS ELEMENTOS TRAZA Y POLISACÁRIDOS DE LA PARED CELULAR DE Sargassum spp. DE ARRIBAZONES

Paulina Annette Ortega Flores (2023, [Tesis de doctorado])

"La frecuencia e intensidad del fenómeno de arribazón de macroalgas marinas ha ido en aumento a nivel mundial. En el Caribe Mexicano, se ha identificado a especies pelágicas de algas pardas del género Sargassum como dominantes en estos arribazones. La gran cantidad de material que arriba a la costa ha resaltado la necesidad de generar información sobre la biología y composición química de las especies presentes en este fenómeno, la cual pueda ser incorporada en futuras estrategias sustentables de aprovechamiento de la biomasa arribada. En el presente estudio se determinaron las concentraciones totales de arsénico (As), cadmio (Cd), plomo (Pb), cobre (Cu), hierro (Fe) y zinc (Zn) en S. fluitans, S. natans I, S. natans VIII, recolectadas mensualmente durante un año, en Puerto Morelos, Quintana Roo, México mediante Espectrofotometría de Absorción Atómica (EAA). Para As, se determinó el contenido de su especie química inorgánica (iAs) en los tres morfotipos mediante voltametría. Adicionalmente, en S. fluitans se determinó el contenido de alginato, fucoidano, ácidos urónicos y sulfatos y se identificaron las variables de contribución significativa en la acumulación de As a partir de un Modelo Lineal Generalizado (GLM). La presencia de As se detectó en el 100% de las muestras; seguido de Fe (98%), Zn (90%), Cu (78%), Pb (71%) y Cd (65%). Las concentraciones máximas obtenidas en las especies pelágicas de Sargassum fueron de 255.20 mg kg-1 para As, 3.75 mg kg-1 para Cd, 17.39 mg kg-1 para Pb, 6.44 mg kg-1 para Cu, 78.27 mg kg-1 para Fe y 33.25 mg kg-1 para Zn. En general, las concentraciones promedio de los elementos analizados se encuentran en rangos previamente reportados para algas pardas. Los elementos As, Cu, Fe y Pb presentaron diferencias estadísticamente significativas entre morfotipos, mientras que los elementos Cd y Zn no. El morfotipo S. natans VIII presentó las concentraciones más elevadas de As respecto a las especies S. fluitans y S. natans I, siendo la temporada de lluvias (julio a octubre) cuando se presentaron las concentraciones más elevadas de este elemento. En cuanto al iAs, este representó del 14.15% al 81.70 % del As total (TotAs), lo que corresponde a 12.69 mg kg-1 a 62. 93 mg kg-1..."

"The frequency and intensity of the seaweed massive influx and arrival phenomenon has been increasing globally. On Mexican shores, has been identified to pelagic species of brown algae of genus Sargassum as dominant in these events. The large amount of material that reaches to the coast, has highlighted the need to generate basic information about the biology and chemical composition of the species present in the arrival phenomenon to be incorporated into future sustainable strategies for the use of Sargassum biomass. In the present study, the total concentrations were determined for arsenic (As), cadmium (Cd), lead (Pb), copper (Cu), iron (Fe) and zinc (Zn) in S. fluitans, S. natans I, S. natans VIII, collected monthly during one year, in Puerto Morelos, Quintana Roo, Mexico. For As, the content of its inorganic chemical species (iAs) was determined. Additionally, in S. fluitans the content of alginate, fucoidan, uronic acids and sulfates was determined and a Generalized Linear Model (GLM) was developed to identify the variables of significant contribution in the accumulation of As. The presence of As was detected in 100% of the samples; followed by Fe (98%), Zn (90%), Cu (78%), Pb (71%) and Cd (65%). The maximum concentrations obtained in the pelagic Sargassum species were 255.20 mg kg-1 for As, 3.75 mg kg-1 for Cd, 17.39 mg kg-1 for Pb, 6.44 mg kg-1 for Cu, 78.27 mg kg-1 for Fe y 33.25 mg kg-1 for Zn. Mean concentrations are in ranges previously reported for brown algae. The elements As, Cu, Fe and Pb showed statistically significant differences between morphotypes, while the elements Cd and Zn did not. The S. natans VIII morphotype presented the highest As concentrations respect to S. fluitans and S. natans I species, being the rainy season (July to October) when the highest concentrations was presented. –Regard to iAs. this represented from 14.15% to 81.70% of the total As (TotAs) which corresponds to 12.69 mg kg-1 to 62. 93 mg kg-1. In S. fluitans, identified the variables: Cu, uronic acids and sulfates from fucoidan, as variables that contribute significantly to the accumulation of As. Monitoring of the diverse components of sargazo is important for the decision making regarding the safe use and exploitation of this resource, as well as, the generation of basic knowledge regarding the process of metal accumulation in Sargassum upwelling."

Mexican Caribbean, Massive influxes, macroalgae, heavy metals Caribe Mexicano, arribazones, macroalgas, metales pesados BIOLOGÍA Y QUÍMICA QUÍMICA QUÍMICA INORGÁNICA METALES METALES

Nitrogen fertilizer application alters the root endophyte bacterial microbiome in maize plants, but not in the stem or rhizosphere soil

Alejandra Miranda Carrazco Yendi Navarro-Noya Bram Govaerts Nele Verhulst Luc Dendooven (2022, [Artículo])

Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the “diversity arrays technology sequencing,” while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled.

Bacterial Community Structure DArT-Seq Bacterial Community Functionality Genes Involved in N Cycling CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA AGRICULTURAL PRACTICES MAIZE RHIZOSPHERE STEMS NITROGEN FERTILIZERS

Bacterial communities in the rhizosphere at different growth stages of maize cultivated in soil under conventional and conservation agricultural practices

Yendi Navarro-Noya Bram Govaerts Nele Verhulst Luc Dendooven (2022, [Artículo])

Farmers in Mexico till soil intensively, remove crop residues for fodder and grow maize often in monoculture. Conservation agriculture (CA), including minimal tillage, crop residue retention and crop diversification, is proposed as a more sustainable alternative. In this study, we determined the effect of agricultural practices and the developing maize rhizosphere on soil bacterial communities. Bulk and maize (Zea mays L.) rhizosphere soil under conventional practices (CP) and CA were sampled during the vegetative, flowering and grain filling stage, and 16S rRNA metabarcoding was used to assess bacterial diversity and community structure. The functional diversity was inferred from the bacterial taxa using PICRUSt. Conservation agriculture positively affected taxonomic and functional diversity compared to CP. The agricultural practice was the most important factor in defining the structure of bacterial communities, even more so than rhizosphere and plant growth stage. The rhizosphere enriched fast growing copiotrophic bacteria, such as Rhizobiales, Sphingomonadales, Xanthomonadales, and Burkholderiales, while in the bulk soil of CP other copiotrophs were enriched, e.g., Halomonas and Bacillus. The bacterial community in the maize bulk soil resembled each other more than in the rhizosphere of CA and CP. The bacterial community structure, and taxonomic and functional diversity in the maize rhizosphere changed with maize development and the differences between the bulk soil and the rhizosphere were more accentuated when the plant aged. Although agricultural practices did not alter the effect of the rhizosphere on the soil bacterial communities in the flowering and grain filling stage, they did in the vegetative stage.

Community Assembly Functional Diversity Intensive Agricultural Practices Plant Microbiome CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA SUSTAINABLE AGRICULTURE TILLAGE SOIL BACTERIA MAIZE

Soil CO2 efflux fluctuates in three different annual seasons in a semideciduous tropical forest in Yucatan, Mexico

El flujo de CO2 del suelo fluctúa en tres temporadas del año en un bosque tropical semideciduo de Yucatán, México

Fernando Arellano-Martín JUAN MANUEL DUPUY RADA ROBERTH ARMANDO US SANTAMARIA José Luis Andrade Torres (2022, [Artículo])

Tropical forest soils store a third of the global terrestrial carbon and control carbon dioxide (CO2) terrestrial effluxes to the atmosphere produced by root and microbial respiration. Soil CO2 efflux varies in time and space and is known to be strongly influenced by soil temperature and water content. However, little is known about the influence of seasonality on soil CO2 efflux, especially in tropical dry forests. This study evaluated soil CO2 efflux, soil temperature, and soil volumetric water content in a semideciduous tropical forest of the Yucatan Peninsula under two sites (flat areas close to and far from hills), and three seasons: dry, wet, and early dry (a transition between the rainy and dry seasons) throughout a year. Additionally, six 24-h periods of soil CO2 efflux were measured within these three seasons. The mean annual soil CO2 efflux was 4±2.2 μmol CO2 m-2 s-1, like the mean soil CO2 efflux during the early dry season. In all seasons, soil CO2 efflux increased linearly with soil moisture, which explained 45% of the spatial-temporal variation of soil CO2 efflux. Soil CO2 efflux was higher close to than far from hills in some months. The daily variation of soil CO2 efflux was less important than its spatial and seasonal variation likely due to small diel variations in temperature. Transition seasons are common in many tropical dry forests, and they should be taken into consideration to have a better understanding of the annual soil CO2 efflux, especially under future climate-change scenarios. © 2022 Mexican Society of Soil Science. All Rights Reserved.

EARLY DRY SEASON SOIL TEMPERATURE SOIL VOLUMETRIC WATER CONTENT TROPICAL DRY FOREST BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA BIOLOGÍA VEGETAL (BOTÁNICA) ECOLOGÍA VEGETAL ECOLOGÍA VEGETAL

Application of ammonium to a N limited arable soil enriches a succession of bacteria typically found in the rhizosphere

Yendi Navarro-Noya Marco Luna_Guido Nele Verhulst Bram Govaerts Luc Dendooven (2022, [Artículo])

Crop residue management and tillage are known to affect the soil bacterial community, but when and which bacterial groups are enriched by application of ammonium in soil under different agricultural practices from a semi-arid ecosystem is still poorly understood. Soil was sampled from a long-term agronomic experiment with conventional tilled beds and crop residue retention (CT treatment), permanent beds with crop residue burned (PBB treatment) or retained (PBC) left unfertilized or fertilized with 300 kg urea-N ha-1 and cultivated with wheat (Triticum durum L.)/maize (Zea mays L.) rotation. Soil samples, fertilized or unfertilized, were amended or not (control) with a solution of (NH4)2SO4 (300 kg N ha-1) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO2 emission, mineral N and the bacterial community were monitored. Application of NH4+ significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH4+ and NO2- was faster in the fertilized soil than in the unfertilized soil. The relative abundance of Nitrosovibrio, the sole ammonium oxidizer detected, was higher in the fertilized than in the unfertilized soil; and similarly, that of Nitrospira, the sole nitrite oxidizer. Application of NH4+ enriched Pseudomonas, Flavisolibacter, Enterobacter and Pseudoxanthomonas in the first week and Rheinheimera, Acinetobacter and Achromobacter between day 7 and 28. The application of ammonium to a soil cultivated with wheat and maize enriched a sequence of bacterial genera characterized as rhizospheric and/or endophytic independent of the application of urea, retention or burning of the crop residue, or tillage.

CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA AMMONIUM CROP RESIDUES WHEAT MAIZE TILLAGE SOIL

Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

CARLOS ABRAHAM GUERRERO RUIZ (2019, [Artículo])

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/ O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection. © 2019 Guerrero et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Article, bacterial gene, bacterial strain, bacterial virulence, comparative study, controlled study, gene cluster, gene identification, genomic island, genotype, nonhuman, phylogenetic tree, sequence analysis, strain identification, Vibrio vulnificus BIOLOGÍA Y QUÍMICA CIENCIAS DE LA VIDA GENÉTICA GENÉTICA

Soil moisture content and maize grain yield under conventional and conservation agriculture practices - results of short term field tests in liselo, Namibia

Christian Thierfelder (2023, [Artículo])

This article focuses on the results from trials developed to monitor the short-term effects of conventionally tilled systems versus CA on soil quality and crop productivity under conditions of the major cropping systems in central, north-central and north-eastern regions of Namibia. Conventional tillage (CT), Minimum tillage (MT), Minimum tillage, mulch (MT-M), Minimum tillage, rotation (MT-R) and Minimum tillage, mulch and rotation (MT-MR) were the primary treatments tested. Significant differences (p≤0.000) among the treatments were observed in the 0-60 cm soil profiles where MT-M plots had the highest soil moisture content (39.8 mm, Standard Error of Mean 0.2815) over the study period. A significant difference (p=0.0206) in grain yield was observed in the second season with CT plots yielding the highest grain yield (3852.3 kg ha-1, standard error of mean 240.35). Results suggest that CA has the potential to increase water conservation and contribute to reduction of the risk of crop failure. Climate change driven degradation under conventional tillage necessitate alternative sustainable tillage methods. Conservation tillage methods and conservation agricultural practices that minimize soil disturbance while maintaining soil cover need to be adopted more locally as viable alternatives to conventional tillage.

Grain Yield Soil Moisture Content CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CONSERVATION AGRICULTURE CONVENTIONAL TILLAGE GRAIN YIELDS SOIL WATER CONTENT MAIZE

The fate of rice crop residues and context-dependent greenhouse gas emissions: Model-based insights from Eastern India

Sonam Sherpa virender kumar Andrew Mcdonald (2024, [Artículo])

Crop residue burning is a common practice in many parts of the world that causes air pollution and greenhouse gas (GHG) emissions. Regenerative practices that return residues to the soil offer a ‘no burn’ pathway for addressing air pollution while building soil organic carbon (SOC). Nevertheless, GHG emissions in rice-based agricultural systems are complex and difficult to anticipate, particularly in production contexts with highly variable hydrologic conditions. Here we predict long-term net GHG fluxes for four rice residue management strategies in the context of rice-wheat cropping systems in Eastern India: burning, soil incorporation, livestock fodder, and biochar. Estimations were based on a combination of Tier 1, 2, and 3 modelling approaches, including 100-year DNDC simulations across three representative soil hydrologic categories (i.e., dry, median, and wet). Overall, residue burning resulted in total direct GHG fluxes of 2.5, 6.1, and 8.7 Mg CO2-e in the dry, median, and wet hydrologic categories, respectively. Relative to emissions from burning (positive values indicate an increase) for the same dry to wet hydrologic categories, soil incorporation resulted in a −0.2, 1.8, or 3.1 Mg CO2-e change in emissions whereas use of residues for livestock fodder increased emissions by 2.0, 2.1, or 2.3 Mg CO2-e. Biochar reduced emissions relative to burning by 2.9 Mg CO2-e in all hydrologic categories. This study showed that the production environment has a controlling effect on methane and, therefore, net GHG balance. For example, wetter sites had 2.8–4.0 times greater CH4 emissions, on average, than dry sites when rice residues were returned to the soil. To effectively mitigate burning without undermining climate change mitigation goals, our results suggest that geographically-target approaches should be used in the rice-based systems of Eastern India to incentivize the adoption of regenerative ‘no burn’ residue management practices.

Soil Carbon Rice Residue Burning Life Cycle Assessment CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA SOIL CARBON RICE LIFE CYCLE GREENHOUSE GASES CLIMATE CHANGE

Expanding the WOFOST crop model to explore options for sustainable nitrogen management: A study for winter wheat in the Netherlands

João Vasco Silva Pytrik Reidsma (2024, [Artículo])

Nitrogen (N) management is essential to ensure crop growth and to balance production, economic, and environmental objectives from farm to regional levels. This study aimed to extend the WOFOST crop model with N limited production and use the model to explore options for sustainable N management for winter wheat in the Netherlands. The extensions consisted of the simulation of crop and soil N processes, stress responses to N deficiencies, and the maximum gross CO2 assimilation rate being computed from the leaf N concentration. A new soil N module, abbreviated as SNOMIN (Soil Nitrogen for Organic and Mineral Nitrogen module) was developed. The model was calibrated and evaluated against field data. The model reproduced the measured grain dry matter in all treatments in both the calibration and evaluation data sets with a RMSE of 1.2 Mg ha−1 and the measured aboveground N uptake with a RMSE of 39 kg N ha−1. Subsequently, the model was applied in a scenario analysis exploring different pathways for sustainable N use on farmers' wheat fields in the Netherlands. Farmers' reported yield and N fertilization management practices were obtained for 141 fields in Flevoland between 2015 and 2017, representing the baseline. Actual N input and N output (amount of N in grains at harvest) were estimated for each field from these data. Water and N-limited yields and N outputs were simulated for these fields to estimate the maximum attainable yield and N output under the reported N management. The investigated scenarios included (1) closing efficiency yield gaps, (2) adjusting N input to the minimum level possible without incurring yield losses, and (3) achieving 90% of the simulated water-limited yield. Scenarios 2 and 3 were devised to allow for soil N mining (2a and 3a) and to not allow for soil N mining (2b and 3b). The results of the scenario analysis show that the largest N surplus reductions without soil N mining, relative to the baseline, can be obtained in scenario 1, with an average of 75%. Accepting negative N surpluses (while maintaining yield) would allow maximum N input reductions of 84 kg N ha−1 (39%) on average (scenario 2a). However, the adjustment in N input for these pathways, and the resulting N surplus, varied strongly across fields, with some fields requiring greater N input than used by farmers.

Crop Growth Models WOFOST CIENCIAS AGROPECUARIAS Y BIOTECNOLOGÍA CROPS NITROGEN-USE EFFICIENCY WINTER WHEAT SOIL WATER