Wastewater irrigation is a common practice for agricultural systems in arid and semiarid zones, which can help to overcome water scarcity and contribute with nutrient inputs. Ammonia-oxidizing ...bacteria (AOB) and archaea (AOA) are key in the transformation of NH4+-N in soil and can be affected by variations in soil pH, EC, N and C content, or accumulation of pollutants, derived from wastewater irrigation. The objective of this study was to determine the changes in the ammonia oxidizing communities in agricultural soils irrigated with wastewater for different periods of time (25, 50, and 100 years), and in rainfed soils (never irrigated). The amoA gene encoding for the catalytic subunit of the ammonia monooxygenase was used as molecular reporter; it was quantified by qPCR and sequenced by high throughput sequencing, and changes in the community composition were associated with the soil physicochemical characteristics. Soils irrigated with wastewater showed up to five times more the abundance of ammonia oxidizers (based on 16S rRNA gene relative abundance and amoA gene copies) than those under rainfed agriculture. While the amoA-AOA: amoA-AOB ratio decreased from 9.8 in rainfed soils to 1.6 in soils irrigated for 100 years, indicating a favoring environment for AOB rather than AOA. Further, the community structure of both AOA and AOB changed during wastewater irrigation compared to rainfed soils, mainly due to the abundance variation of certain phylotypes. Finally, the significant correlation between soil pH and the ammonia oxidizing community structure was confirmed, mainly for AOB; being the main environmental driver of the ammonia oxidizer community. Also, a calculated toxicity index based on metals concentrations showed a correlation with AOB communities, while the content of carbon and nitrogen was more associated with AOA communities. The results indicate that wastewater irrigation influence ammonia oxidizers communities, manly by the changes in the physicochemical environment.
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DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Abstract
Rincon de Parangueo (RP) is a Quaternary maar crater located in the Michoacan‐Guanajuato Volcanic Field in central Mexico. Like other volcanic craters in the region, the central part was ...occupied by an endorheic lacustrine system. As a consequence of extensive groundwater extraction, the perennial lake started a gradual desiccation process and now the remnant ponds host a highly saline–alkaline ecosystem. The stratigraphic record indicates an exceptional and long‐term sedimentation of carbonate microbialites. Previous studies based on the 16S rRNA gene have shown that microbial communities have a widespread presence in the crater at the microbialites, the remaining saline ponds, superficial soils and below the surface. To understand the possible role of the microbial communities that generate these biogeological structures, novel analytical methods to resolve the amplicon datasets and their microbial metabolic potential were used.
We describe in detail the relationship between the microbial communities, the evolution of physicochemical parameters, and carbonate morphology, in four micro‐environments. A 16S rRNA gene sequencing dataset from previous publications was re‐analysed using an ASV‐based bioinformatic pipeline to identify new insights into the microbial assemblage. Finally, a taxon‐based metabolic profile was used to predict the potential metabolic contribution of the prokaryotic community.
Results indicated a refinement in terms of community composition using the ASV‐based bioinformatic methods. Functional profiling through 16S rRNA gene‐based analysis suggested metabolisms associated with carbonate precipitation, indicating a broad potential for microbially mediated carbonate precipitation (e.g., carbon fixation and photosynthesis). The possibility of biogenic methane gas production by methanogenic microorganisms was recognised, supporting the estimated flow of methane on the surface soils.
The lacustrine evolution over the last years and the extreme physicochemical characteristics of RP have an impact on the microbial community structure. Prokaryotic community and metabolic potential results from RP coincide with the diversity and abundance of microbial communities and functional metabolisms reported from other microbialite‐forming lakes along the Trans Mexican Volcanic Belt. The identification of important possible phylotypes involved in carbonate precipitation might be an important factor in considering RP microbialites as active calcifying entities.
These findings provide novel insights into the potential key role of metabolic pathways driving the process of carbonate precipitation inside RP and evidence of its importance as a microbial biodiversity hotspot in Mexico.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Abstract
Microbialites have played an important role in the early history of life on Earth. Their fossilized forms represent the oldest evidence of life on our planet dating back to 3500 Ma. Extant ...microbialites have been suggested to be highly productive and diverse communities with an evident role in the cycling of major elements, and in contributing to carbonate precipitation. Although their ecological and evolutionary importance has been recognized, the study of their genetic diversity is yet scanty. The main goal of this study was to analyse microbial genetic diversity of microbialites living in different types of environments throughout Mexico, including desert ponds, coastal lagoons and a crater-lake. We followed a pyrosequencing approach of hypervariable regions of the 16S rRNA gene. Results showed that microbialite communities were very diverse (H′ = 6–7) and showed geographic variation in composition, as well as an environmental effect related to pH and conductivity, which together explained 33% of the genetic variation. All microbialites had similar proportions of major bacterial and archaeal phyla.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Folia are speleothems that resemble bells, inverted cups, or bracket fungi, and whose origins are still controversial. Cenote Zapote (an underwater cave) in the Yucatán Peninsula (México), is home to ...some of the largest folia reported to date. These speleothems are currently growing in an active underwater system, meaning this site offers an excellent opportunity to constrain the different formation models proposed for folia, which have traditionally relied on inactive examples. In Cenote Zapote, folia are closely related to bubble trails and cupolas, suggesting an underwater CO2-degassing process. In thin section, they display a succession of columnar-open and columnar-elongated endings in micrite-dendritic fabrics. Our petrographic and geochemical results demonstrate the abiotic origin of these folia and indicate carbonate precipitation from cold water by CO2 degassing below the water table that started at least 5,210 yrs BP. We conclude that these folia formed as a result of subaqueous calcite precipitation around CO2 bubbles trapped below overhanging walls of the cave. The sequential alternation of columnar and micritic fabrics can be explained by changes in the position of the halocline and H2S-rich water mass while the exceptional size is the result of carbonate precipitation from waters saturated in CaCO3 during thousans of years. Then we propose the classification of these speleothems as a subtype of folia. This subtype could be named Hells Bells, respecting its original description.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Due to the high concentration of pollutants, swine wastewater needs to be treated prior to disposal. The combination of anaerobic and aerobic technologies in one hybrid system allows to obtain higher ...removal efficiencies compared to those achieved via conventional biological treatment, and the performance of a hybrid system depends on the microbial community in the bioreactor. Here, we evaluated the community assembly of an anaerobic-aerobic hybrid reactor for swine wastewater treatment. Sequencing of partial 16S rRNA coding genes was performed using Illumina from DNA and retrotranscribed RNA templates (cDNA) extracted from samples from both sections of the hybrid system and from a UASB bioreactor fed with the same swine wastewater influent. Proteobacteria and Firmicutes were the dominant phyla and play a key role in anaerobic fermentation, followed by Methanosaeta and Methanobacterium. Several differences were found in the relative abundances of some genera between the DNA and cDNA samples, indicating an increase in the diversity of the metabolically active community, highlighting Chlorobaculum, Cladimonas, Turicibacter and Clostridium senso stricto. Nitrifying bacteria were more abundant in the hybrid bioreactor. Beta diversity analysis revealed that the microbial community structure significantly differed among the samples (p < 0.05) and between both anaerobic treatments. The main predicted metabolic pathways were the biosynthesis of amino acids and the formation of antibiotics. Also, the metabolism of C5-branched dibasic acid, Vit B5 and CoA, exhibited an important relationship with the main nitrogen-removing microorganisms. The anaerobic-aerobic hybrid bioreactor showed a higher ammonia removal rate compared to the conventional UASB system. However, further research and adjustments are needed to completely remove nitrogen from wastewater.
•A hybrid anaerobic-aerobic reactor was evaluated for swine wastewater treatment.•The hybrid reactor enhanced NH4+ and P removal compared to a control UASB reactor.•Bacterial composition was significantly different from anaerobic-hybrid to the UASB reactor.•Methanosaeta was predominant in all samples, especially in the UASB.•The relative abundances of total and metabolically active genera differed.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
Coralline algae are worldwide carbonate builders, considered to be foundational species and biodiversity hotspots. Coralline habitats face increasing pressure from human activities and effects ...related to Global Change, yet their ecological properties and adaptive responses remain poorly understood. The relationships of the algal microbiota with the mineral bioconstructions, as well as plasticity and resilience of coralline holobionts in a changing environment, are of particular interest. In the Gulf of California, Neogoniolithon trichotomum (Rhodophyta) is the main carbonate builder in tidal pools. We performed a multi-disciplinary assessment of the N. trichotomum microstructure using XRD, SEM microscopy and SR-FTIR spectromicroscopy. In the algal perithallus, magnesium-calcite and aragonite were spatially segregated and embedded in a polysaccharide matrix (rich in sulfated polysaccharides). Mg-calcites (18–19 mol% Mg) were the main mineral components of the thallus overall, followed by iron carbonates related to dolomite (ankerite) and siderite. Minerals of late evaporitic sequences (sylvite and bischofite) were also present, suggesting potential halophilic microenvironments within the algal thalli. The diverse set of abundant halophilic, halotolerant and oligotrophic taxa, whose abundance increase in the summer, further suggests this condition. We created an integrated model, based on environmental parameters and the microbiota distribution, that identified temperature and nutrient availability (particularly nitrate and silicate) as the main parameters related to specific taxa patterns. Among these, Hahella, Granulossicoccus, Ferrimonas, Spongiibacteraceae and cyanobacterial Xenococcaceae and Nostocaceae change significantly between seasons. These bacterial components might play relevant roles in algal plasticity and adaptive responses to a changing environment. This study contributes to the understanding of the interplay of the prokaryotic microbiota with the mineral microenvironments of coralline algae. Because of their carbonates with potential resistance to dissolution in a higher pCO2 world and their seasonally dynamic bacteria, coralline algae are relevant targets to study coastal resilience and carbonated systems responses to changing environments.
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•The interplay of microorganisms and algal mineral bioconstructions remains poorly understood.•Carbonates rich in Fe and Mg found make CA relevant targets to study coastal resilience.•Halophiles and evaporite minerals concurrently suggest halophilic microenvironments in the thallus.•Bacterial microbiota correlated significantly with temperature and nutrients.•Key bacteria might play relevant roles in adaptive responses of coralline algae.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
The members of the Phyllostomidae, the New-World leaf-nosed family of bats, show a remarkable evolutionary diversification of dietary strategies including insectivory, as the ancestral trait, ...followed by appearance of carnivory and plant-based diets such as nectarivory and frugivory. Here we explore the microbiome composition of different feeding specialists: insectivore Macrotus waterhousii, sanguivore Desmodus rotundus, nectarivores Leptonycteris yerbabuenae and Glossophaga soricina, and frugivores Carollia perspicillata and Artibeus jamaicensis. The V4 region of the 16S rRNA gene from three intestinal regions of three individuals per species was amplified and community composition and structure was analyzed with α and β diversity metrics. Bats with plant-based diets had low diversity microbiomes, whereas the sanguivore D. rotundus and insectivore M. waterhousii had the most diverse microbiomes. There were no significant differences in microbiome composition between different intestine regions within each individual. Plant-based feeders showed less specificity in their microbiome compositions, whereas animal-based specialists, although more diverse overall, showed a more clustered arrangement of their intestinal bacterial components. The main characteristics defining microbiome composition in phyllostomids were species and feeding strategy. This study shows how differences in feeding strategies contributed to the development of different intestinal microbiomes in Phyllostomidae.
The soil of the former lake Texcoco is an ‘extreme’ alkaline saline soil with pH > 10 and electrolytic conductivity (EC) > 150 dS m
−1. These conditions have created a unique environment. Application ...of wastewater sludge to Texcoco soil showed that large amounts of NH
4
+ were immobilized, NO
3
− was reduced aerobically, NO
2
− was formed and the mineralization of the organic material in the sludge was inhibited. A series of experiments were initiated to study the processes that inhibited the decomposition of organic material and affected the dynamics of mineral N. The large EC and pH inhibited the decomposition of easily decomposable organic material such as glucose and maize, although cellulolytic activity was observed in soil with pH 9.8 and EC 32.7 dS m
−1. The high soil pH favoured NH
3 volatilization of approximately 50 mg N kg
−1 soil within a day and a similar amount could be fixed on the soil matrix due to the dispersed minerals and their volcanic origin. Soil microorganisms immobilized large amounts of NH
4
+ within a day when glucose was added to soil in excess of what was required for metabolic activity. Removal of NO
3
− from soil amended with glucose was not inhibited by 100% O
2 and NH
4
+ indicating that the contribution of denitrification and assimilatory reduction to the reduction of NO
3
− was minimal while the formation of NO
2
− was not inhibited by 0.1% acetylene, known to inhibit nitrification. Additionally, the reduction of NO
3
− in the glucose-amended alkaline saline Texcoco soil was followed by an increase in the amount of NH
4
+, which could not be due to denitrification. It was concluded that the reduction of NO
3
− and the formation of NO
2
− and NH
4
+ in the glucose-amended soil was a result of aerobic NO
3
− reduction. A phylogenetic analysis of the archaeal community in the soil of the former lake Texcoco showed that some of the clones identified were capable of reducing NO
3
− aerobically to NO
2
− when glucose was added. A study of the diversity of the bacterial dissimilatory and respiratory nitrate-reducing communities indicated that bacteria could have contributed to the process.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UL, UM, UPUK, ZRSKP
Acid mine drainage (AMD) causes major environmental problems and consequently, several treatments are proposed, favoring the passive systems because of their many advantages. The main goal of these ...procedures is the neutralization and removal of potentially toxic elements (PTE), yet little is known about the changes in the microbial assemblages in response to the hydrochemical variations during the treatments. Therefore, the main objective of this research was to determine the changes in the diversity and structure of the prokaryotic assemblages in a hybrid abiotic and biological (wetland) passive treatment system. The 16S rRNA gene survey showed that the AMD coming from the mine (pH 2.6) was mainly composed of acidophilic genera such as Acidithiobacillus, Leptospirillum, Ferritrophicum, and Cuniculiplasma (up to 76 % relative abundance). In the abiotic treatment, Acidiphilium was dominant in the sections with limestone filters (pH 2.2–4.8), followed by Limnobacter in the subsequent dolomite/limestone and phosphoric rock filters (pH 5.2–5.8). In these abiotic passive treatment sections, the microbial assemblage showed a limited diversity and richness. However, when the treated AMD reached the two final wetlands (pH ~6.8), the microbial diversity and richness increased, suggesting that further bioattenuation mechanisms might be occurring. Limnobacter and Novosphingobium were the main bacterial genera in the water samples of the wetland sections (Arundo donax). These changes in the composition of the microbial assemblages were highly correlated with the pH and Eh values during the treatment (p-value <0.001); however, the concentration of metal(loid)s such as Al, Cd, Fe, Mn, Ni, and Zn were also significantly related (p-value <0.05). In conclusion, the studied passive AMD treatment system enhanced the chemical quality of the treated AMD, showing high removal efficiencies for Al and Fe (> 99 %), and increasing the microbial diversity and richness in the effluent.
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•AMD passive treatments can integrate abiotic and biotic processes efficiently.•Prokaryotes in the treated AMD are highly correlated with pH and Eh values.•Constructed wetlands increase the prokaryotic diversity in treated AMDs.•Hybrid AMD treatments improve the chemical and biological water quality.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPUK, ZAGLJ, ZRSKP
This study investigates the community composition, structure, and abundance of sulfate-reducing microorganisms (SRM) in surficial sediments of the Northwestern Gulf of Mexico (NWGoM) along a ...bathymetric gradient. For these purposes, Illumina sequencing and quantitative PCR (qPCR) of the dissimilatory sulfite reductase gene beta subunit (
dsrB
gene) were performed. Bioinformatic analyses indicated that SRM community was predominantly composed by members of
Proteobacteria
and
Firmicutes
across all the samples. However,
Actinobacteria
,
Thermodesulfobacteria
, and
Chlorobi
were also detected. Phylogenetic analysis indicated that unassigned
dsrB
sequences were related to Deltaproteobacteria and Nitrospirota superclusters,
Euryarchaeota
, and to environmental clusters. PCoA ordination revealed that samples clustered in three different groups. PERMANOVA indicated that water depth, temperature, redox, and nickel and cadmium content were the main environmental drivers for the SRM communities in the studied sites. Alpha diversity and abundance of SRM were lower for deeper sites, suggesting decreasing sulfate reduction activity with respect to water depth. This study contributes with the understanding of distribution and composition of
dsrAB
-containing microorganisms involved in sulfur transformations that may contribute to the resilience and stability of the benthic microbial communities facing metal and hydrocarbon pollution in the NWGoM, a region of recent development for oil and gas drilling.
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EMUNI, FZAB, GEOZS, IJS, IMTLJ, KILJ, KISLJ, MFDPS, NUK, OILJ, PNG, SAZU, SBCE, SBJE, SBMB, SBNM, UKNU, UL, UM, UPUK, VKSCE, ZAGLJ
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