•Review on the use of earthworms in the remediation of contaminants from soil.•Remediation efficiency depends on contaminant concentration.•Efficiency also depends on earthworm abundance, species and ...colonization capacity.•Contaminant removal stimulated by earthworm-mediated effects on microbial activity.•The use of earthworms in the remediation of soil also has its limitations.
Earthworms can accelerate the removal of contaminants from soil. Earthworms change the physical and chemical properties of soil by mixing it with organic material and through their burrowing they improve aeration and render contaminants available for microorganisms. The presence of earthworms in contaminated soil indicate that they can survive a wide range of different organic contaminants, such as pesticides, herbicides, polycyclic aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), and crude oil, at least when concentrations of the contaminant are not too high. The improvement of the soil due to their activity and the microorganisms in their digestive track can contribute to the accelerated removal of contaminants from soil, but sometimes their casts adsorb the pollutant so that its dissipation is delayed. There are limits, however, on how earthworms can be used to remediate soil, which will be discussed in this review.
Microorganisms are often applied as biofertilizer to crops to stimulate plant growth, increase yields and reduce inorganic N application. The survival and proliferation of these allochthonous ...microorganisms in soil is a necessary requisite for them to promote plant growth. We applied a sterilized or unsterilized not commercialized bacterial consortium mixed with cow manure leachate used by a farmer as biofertilizer to maize (Zea mays L.) in a greenhouse experiment, while maize development and the bacterial community structure was determined just before the biofertilizer was applied a first time (day 44), after three applications (day 89) and after six application at the end of the experiment (day 130). Application of sterilized or unsterilized biofertilizer with pH 4.3 and 864 mg NH
-N kg
had no significant effect on maize growth. The application of the biofertilizer dominated by Lactobacillus (relative abundance 11.90%) or the sterilized biofertilizer changed the relative abundance of a limited number of bacterial groups, i.e. Delftia, Halomonas, Lactobacillus and Stenotrophomonas, without altering significantly the bacterial community structure. Cultivation of maize, however, affected significantly the bacterial community structure, which showed large significant variations over time in the cultivated and uncultivated soil. It was concluded that the bacteria applied as a biofertilizer had only a limited effect on the relative abundance of these groups in uncultivated or soil cultivated with maize.
Rhizosphere and root endophytic bacteria are crucial for plant development, but the question remains if their composition is similar and how environmental conditions, such as water content, affect ...their resemblance. Ricinus communis L., a highly drought resistant plant, was used to study how varying soil water content affected the bacterial community in uncultivated, non-rhizosphere and rhizosphere soil, and in its roots. Additionally, the bacterial community structure was determined in the seeds of R. communis at the onset of the experiment. Plants were cultivated in soil at three different watering regimes, i.e. 50% water holding capacity (WHC) or adjusted to 50% WHC every two weeks or every month. Reducing the soil water content strongly reduced plant and root dry biomass and plant development, but had little effect on the bacterial community structure. The bacterial community structure was affected significantly by cultivation of R. communis and showed large variations over time. After 6 months, the root endophytic bacterial community resembled that in the seeds more than in the rhizosphere. It was found that water content had only a limited effect on the bacterial community structure and the different bacterial groups, but R. communis affected the bacterial community profoundly.
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
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 (NH
)
SO
(300 kg N ha
) and were incubated aerobically at 25 ± 2 °C for 56 days, while CO
emission, mineral N and the bacterial community were monitored. Application of NH
significantly increased the C mineralization independent of tillage-residue management or N fertilizer. Oxidation of NH
and NO
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 NH
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.
Biosolids are a by-product of wastewater treatment, and their nutritional composition makes them ideal for fertilizing crops. However, pre-treatments, such as conditioning and/or (vermi)composting, ...are often required to stabilize the product and remove pathogens. Biosolids, cow manure, and a 50–50% mixture were conditioned for 21 days, composted or vermicomposted with
Eisenia fetida
(Savigny 1826) for 28 days, and applied to soil cultivated with wheat (
Triticum
sp. L.), while emissions of nitrous oxide (N
2
O), methane (CH
4
), and carbon dioxide (CO
2
) were monitored. Emissions of CH
4
were large from the biosolid and N
2
O from the cow manure during conditioning. Emissions of CH
4
remained high during (vermi)composting of the biosolids, while the emissions of N
2
O from the cow manure dropped. The addition of
E. fetida
did not affect the emissions of greenhouse gases during (vermi)composting. The emission of N
2
O was higher when (vermi)composted biosolid was applied to soil cultivated with wheat than when (vermi)composted cow manure was applied. The global warming potential (GWP) of the sum of the emitted greenhouse gases (GHG) during conditioning, (vermi)composting, and when the final product was applied to soil was 3 times larger from the cow manure than from the biosolid, but mixing biosolid with cow manure eliminated that difference. It was concluded that mixing biosolid with cow manure might be a simple way to reduce the GWP of the emitted GHG during storage, (vermi)composting, and when applied to soil.
•Tillage-crop residue management affected soil organic C concentration.•Soil organic C, fertilizer and tillage-crop residue management defined the bacterial community.•Agronomic practices did not ...alter C or N mineralization of added plant material.•Tillage-crop residue management defined bacterial population capable to degrade wheat plant residue.
Conservation agriculture is a sustainable alternative to conventional agriculture. However, little is known about their effect on the environment and on the soil microbial community. It was established as a hypothesis that the bacterial community structure would be defined by the different agronomic practices. The objective of this study was, therefore, to investigate how crop residue management, tillage and fertilizer application affected the bacterial community and those groups involved in the degradation of applied plant residues, and increase the knowledge to predict the sustainability of a soil under a specific agronomic practice. Samples from an arable soil from the state of Sonora (México), i.e. Hyposodic Vertisol (Calcaric, Chromic) (IUSS Working Group, 2007), cultivated with wheat (Triticum spp.) and maize (Zea mays L.) in succession on conventionally tilled beds (CTB) with crop residue incorporated, permanent beds (PB) with residue burned or retained, left unfertilized or fertilized (300kgNha−1 for wheat and 103kgNha−1 for maize) was improved with dried young wheat plants to stimulate microbial growth, while the bacterial community structure and C and N mineralization were monitored in an aerobic incubation of 56 days. The soil organic C was significantly higher in the PB-residue retained treatments (average 13.1gkg−1 dry soil) compared with PB-residue burned (average 9.9gkg−1 dry soil) or CTB-residue incorporated (average 10.5gkg−1 dry soil), while pH and EC were significantly higher in the PB-residue burned (averages 8.85 and 1.06dSm−1) compared with the fertilized or unfertilized soil in PB-residue retained (averages 8.65 and 0.78dSm−1) or CTB-residue incorporated (averages 8.75 and 0.95dSm−1). In the unimproved soil, we found a significant effect of soil organic C, application of N fertilizer (highly significant on Nitrosovibrio) and tillage-residue management (principally in fertilized soil) on the bacterial community structure, but not in the improved soil. Treatment had no significant effect on the decomposition of the applied organic material, and on average 48% and 9.4% of the applied C and N, respectively, were mineralized in 56 days. Improvement of soil with wheat plant material increased mainly the relative abundance of Actinobacteria and Firmicutes and decreased a wide range of bacterial groups. On the bacterial level of genus, tillage-residue management was the most important defining factor of the bacterial community inducing differences in the genera involved in the degradation of applied plant material, i.e. Promicromonospora, Bacillus, Agromyces, Streptomyces, Sinorhizobium and Lysobacter, in different treatments. It was found that nitrogen fertilization and tillage-crop residue management defined the soil bacterial community structure in the unimproved soil, but were less determinant in improved soil, and these results supported the hypothesis tested. It was concluded that all the factors tested, i.e. tillage, crop-residue management and fertilizer application, affect the soil bacterial community structure, while the mineralization potential of the soil was preserved. This study contributes to our understanding of how soil use and management practices define the soil bacterial community structure.
High-altitude ecosystems are extreme environments that generate specific physiological, morphological, and behavioral adaptations in ectotherms. The shifts in gut microbiota of the ectothermic hosts ...as an adaptation to environmental changes are still largely unknown. We investigated the food ingested and the bacterial, fungal, and protistan communities in feces of the lizard Sceloporus grammicus inhabiting an altitudinal range using metabarcoding approaches.
The bacterial phyla Bacteroidetes and Firmicutes, and the genera Bacteroides and Parabacteroides dominated the core fecal bacteriome, while Zygomycota and Ascomycota, and the species Basidiobolus ranarum and Basidiobolus magnus dominated the core fecal mycobiome. The diet of S. grammicus included 29 invertebrate families belonging to Arachnida, Chilopoda, and Insecta. The diversity and abundance of its diet decreased sharply at high altitudes, while the abundance of plant material and Agaricomycetes was significantly higher at the highest site. The composition of the fecal microbiota of S. grammicus was different at the three altitudes, but not between females and males. Dietary restriction in S. grammicus at 4150 m might explain the high fecal abundance of Akkermansia and Oscillopira, bacteria characteristic of long fasting periods, while low temperature favored B. magnus. A high proportion of bacterial functions were digestive in S. grammicus at 2600 and 3100, while metabolism of aminoacids, vitamins, and key intermediates of metabolic pathways were higher at 4150 m. Different assemblages of fungal species in the lizard reflect differences in the environments at different elevations. Pathogens were more prevalent at high elevations than at the low ones.
Limiting food resources at high elevations might oblige S. grammicus to exploit other food resources and its intestinal microbiota have degradative and detoxifying capacities. Sceloporus grammicus might have acquired B. ranarum from the insects infected by the fungus, but its commensal relationship might be established by the quitinolytic capacities of B. ranarum. The mycobiome participate mainly in digestive and degradative functions while the bacteriome in digestive and metabolic functions.
Agricultural practices affect the bacterial community structure, but how they determine the response of the bacterial community to drought, is still largely unknown. Conventional cultivated soil, ...i.e., inorganic fertilization, tillage, crop residue removal and maize (
L.) monoculture, and traditional organic farmed soil "milpa," i.e., minimum tillage, rotation of maize, pumpkin (
sp.) and beans (
L.) and organic fertilization were sampled. Both soils from the central highlands of Mexico were characterized and incubated aerobically at 5% field capacity (5%FC) and 100% field capacity (FC) for 45 days, while the C and N mineralization, enzyme activity and the bacterial community structure were monitored. After applying the different agricultural practices 3 years, the organic C content was 1.8-times larger in the milpa than in the conventional cultivated soil, the microbial biomass C 1.3-times, and C and N mineralization 2.0-times (mean for soil incubated at 5%FC and FC). The dehydrogenase, activity was significantly higher in the conventional cultivated soil than in the milpa soil when incubated at 5%FC, but not when incubated at FC. The relative abundance of Gemmatimonadetes was larger in the conventional cultivated soil than in the milpa soil in soil both at 5%FC and FC, while that of Bacteroidetes showed an opposite trend. The relative abundance of other groups, such as Nitrospirae and Proteobacteria, was affected by cultivation technique, but controlled by soil water content. The relative abundance of other groups, e.g., FBP, Gemmatimonadetes and Proteobacteria, was affected by water content, but the effect depended on agricultural practice. For soil incubated at FC, the xenobiotics biodegradation and metabolism related functions were higher in the milpa soil than in the conventional cultivated soil, and carbohydrate metabolism showed an opposite trend. It was found that agricultural practices and soil water content had a strong effect on soil characteristics, C and N mineralization, enzyme activity, and the bacterial community structure and its functionality. Decreases or increases in the relative abundance of bacterial groups when the soil water content decreased, i.e., from FC to 5%FC, was defined often by the cultivation technique, and the larger organic matter content in the milpa soil did not prevent large changes in the bacterial community structure when the soil was dried.
Wells used for drinking water often have a large biomass and a high bacterial diversity. Current technologies are not always able to reduce the bacterial population, and the threat of pathogen ...proliferation in drinking water sources is omnipresent. The environmental conditions that shape the microbial communities in drinking water sources have to be elucidated, so that pathogen proliferation can be foreseen. In this work, the bacterial community in nine water wells of a groundwater aquifer in Northern Mexico were characterized and correlated to environmental characteristics that might control them. Although a large variation was observed between the water samples, temperature and iron concentration were the characteristics that affected the bacterial community structure and composition in groundwater wells. Small increases in the concentration of iron in water modified the bacterial communities and promoted the growth of the ironoxidizing bacteria Acidovorax. The abundance of the genera Flavobacterium and Duganella was correlated positively with temperature and the Acidobacteria Gp4 and Gp1, and the genus Acidovorax with iron concentrations in the well water. Large percentages of Flavobacterium and Pseudomonas bacteria were found, and this is of special concern as bacteria belonging to both genera are often biofilm developers, where pathogens survival increases.
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