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Microbialites are sedimentary structures that represent modern models of the oldest life forms, stromatolites (

Eutrophication is a global problem causing the reduction of water quality and the loss of ecosystem goods and services. The lakes of the “Lagunas de Montebello” National Park (LMNP), Chiapas, Mexico, not only represent unique and beautiful natural scenic sites in southern Mexico but are also a national protected area and RAMSAR site. Unfortunately, some of these lakes started showing eutrophication signs since 2003. Anthropogenic activities (e.g., land-use change from forested to agricultural and urban development) are leading to water quality and trophic state alterations of the lakes of the LMNP. This study shows the results of a coupled limnological characterization and high-throughput sequencing of the V4 hypervariable region of the 16S rRNA gene to analyze the microbial composition of the water column in a set of oligotrophic and eutrophic lakes. Chlorophyll a (Chl-a) was the main environmental parameter correlated with the trophic conditions of the lakes. Although the microbial diversity was similar, the microbial composition changed significantly from oligo to eutrophic lakes. Proteobacteria, Firmicutes, and Cyanobacteria were the main components of oligotrophic lakes, and Cyanobacteria, Proteobacteria, and Bacteroidetes of eutrophic lakes. While Acinetobacter (Proteobacteria) and Cyanobium (a unicellular cyanobacterium) dominated in oligotrophic lakes, the filamentous, bloom-forming, and toxin-producing cyanobacteria Planktothrix was the dominant genus in eutrophic lakes. High-throughput sequencing allowed the detection of changes in the composition of the microbial component in oligotrophic lakes, suggesting a shift towards eutrophication, highlighting the relevance of sensitive monitoring protocols of these ecosystems to implement remediation programs for eutrophicated lakes and conservation strategies for those yet pristine.

BackgroundHigh-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 lizardSceloporus grammicusinhabiting an altitudinal range using metabarcoding approaches.ResultsThe bacterial phylaBacteroidetesandFirmicutes, and the generaBacteroidesandParabacteroidesdominated the core fecal bacteriome, whileZygomycotaandAscomycota, and the speciesBasidiobolus ranarumandBasidiobolus magnusdominated the core fecal mycobiome. The diet ofS.grammicusincluded 29 invertebrate families belonging toArachnida,Chilopoda, andInsecta. The diversity and abundance of its diet decreased sharply at high altitudes, while the abundance of plant material andAgaricomyceteswas significantly higher at the highest site. The composition of the fecal microbiota ofS.grammicuswas different at the three altitudes, but not between females and males. Dietary restriction inS.grammicusat 4150 m might explain the high fecal abundance ofAkkermansiaandOscillopira, bacteria characteristic of long fasting periods, while low temperature favoredB.magnus. A high proportion of bacterial functions were digestive inS.grammicusat 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.ConclusionsLimiting food resources at high elevations might obligeS.grammicusto exploit other food resources and its intestinal microbiota have degradative and detoxifying capacities.Sceloporus grammicusmight have acquiredB.ranarumfrom the insects infected by the fungus, but its commensal relationship might be established by the quitinolytic capacities ofB.ranarum.The mycobiome participate mainly in digestive and degradative functions while the bacteriome in digestive and metabolic functions.

The “Hoya del Rincon de Parangueo (HRP)” is a maar that contained a perennial alkaline lake that drained in the 1980s so that a sediment with high pH and extreme salinity remained. The aim of this work was to determine how the bacterial and archaeal community was controlled by these extreme conditions. Sediment samples were collected from the 0–20-cm layer along a crater-wide transect. Physicochemical characteristics and the archaeal and bacterial community were determined by analysis of the 16S rRNA through Illumina sequencing. The sediment samples had a pH 10 and an electrolytic conductivity (EC) that ranged from 29.8 to 74.4 dS m−1. Three archaeal and 37 bacterial phyla were detected with Euryarchaeota (relative abundance 62.7 ± 17.6%) dominating the Archaea, and Proteobacteria (28.2 ± 10.7%) and Actinobacteria (21.1 ± 6.4%) the Bacteria. The most abundant archaeal genus was Candidatus Nitrososphaera while Euzebya, Halomonas, KSA1 and Planctomycetes dominated the bacterial gene. Thaumarchaeota were enriched in sediment samples with a higher Pb content and Euryarchaeota in sediment with a higher Mg content, while Crenarchaeota and Candidatus Nitrososphaera were enriched in sediment with a higher sand, total N and organic C content. Proteobacteria were enriched in sediment with a higher organic C and total N, Si and sand content, while Bacteroidetes and Planctomycetes in sediment with a higher water holding capacity and clay and Mg content. Members of KSA1 and Euzebya were enriched in sediment with a lower EC, organic C and total N content. Although a large number of bacterial and archaeal groups were correlated significantly with a range of sediment characteristics, the sediment characteristics explained the variation of only two bacterial groups > 50% (TM6 and Desulfonatronospira) using the machine learning tool randomForest and none of the archaeal groups. Archaeal and bacterial functional guilds were dominated by ammonium oxidation and nitrite reduction. Although the different sediment samples were dominated often by similar bacterial and archaeal groups, the measured sediment characteristics explained little of the variation found between the sampling points. The high bacterial and archaeal diversity indicated that the site might be a source of unclassified species and phylotypes with specific metabolic capacities involved in the N and S cycles.

Halophiles can be found in hypersaline environments and they can synthesize products of industrial interest. Method: In this work, 37 bacterial strains were isolated from the sediment of a dried-out maar of the “Hoya Rincón de Parangueo” (Mexico) on different culture media with 20% NaCl and pH 9, while potential industrial extracellular enzymes were determined. Results: Eight genera Salsuginibacillus, Alkalibacillus, Bacillus, Staphylococcus, Oceanobacillus, Halomonas and Nesterenkonia besides 15 distinct species belonging to Actinobacteria, Firmicutes and Proteobacteria were identified. The L371, LTA7 and SU3 isolates produced proteases, M20, L5, L7, L8, Y1, Y2, M3, M9 and RA lipases, LTA4 and SU3 amylases, while LTA7, Y2, M5, M9 and RA caseinases with enzymatic activity at pH 9. Production of siderophore was found in 17 isolates. Discussion or Conclusion: It is reported for the first experimental evidence of siderophores production by N. alba, Alkalibacillus and Oceanobacillus at 6% NaCl (w/v). Isolates RE, RG1, RG2, RH1, RA and I11 showed 2.8% to 4.1% genetic distance with Nesterenkonia species and might represent new species.

Extant stromatolites have been considered ecological similes to their ancient counterparts. We now know that these microbial assemblages are composed of a great diversity of microbes, which couple and intertwine their metabolic capabilities to create self-sustained microbial ecosystems. Presently, stromatolites thrive in a vast diversity of aquatic environments including freshwater, hypersaline, coastal lagoons, alkaline lakes, oligotrophic pools, abandoned pits, few marine systems, and brackish waters. In this chapter, we will summarize the research that has been done in two stromatolite-harboring sites in Mexico: the alkaline crater-lake Alchichica and the oligotrophic karstic coastal lagoon of Bacalar. Alchichica is located in the Transvolcanic belt in Central Mexico. It is a maar-alkaline crater lake (salinity 8.5 gl−1, pH 9.5) with water chemistry determined by high contents of carbonates, sodium, a high Mg/Ca ratio, and particularly low Ca2+ concentrations (~0.3 mM). Two main stromatolite-types, as defined by mineralogy, texture, and microbial composition, develop along its periphery from surface to over 30 m in depth. Alchichica is a modern environment that resembles Precambrian oceanic conditions. Stromatolites from Alchichica have been dated radiometrically in ~1.1–2.8 ka BP. Bacalar is a coastal lagoon located in the Yucatan Peninsula, which is a carbonate platform that emerged above sea level during the Oligocene. The Bacalar lagoon has high carbonate concentrations as a result of the influx of groundwater (salinity 1.2 gl−1, pH 7.6–8.3). It holds the largest freshwater stromatolite structures known, which have been radiometrically dated in ~6.8–9.2 ka BP. Their mineralogy, shape, and texture are similar along the lagoon’s coast, but microbial composition changes, possibly due to anthropogenic impact.

Author(s): Yanez-Montalvo, Alfredo; Aguila, Bernardo; Gomez-Acata, Elizabeth S; Beltran, Yislem; Valdespino-Castillo, Patricia M; Centeno, Carla M; Falcon, Luisa I

Microorganisms in aerobic granules formed in sequencing batch reactors (SBR) remove contaminants, such as xenobiotics or dyes, from wastewater. The granules, however, are not stable over time, decreasing the removal of the pollutant. A better understanding of the granule formation and the dynamics of the microorganisms involved will help to optimize the removal of contaminants from wastewater in a SBR. Sequencing the 16S rRNA gene and internal transcribed spacer PCR amplicons revealed that during the acclimation phase the relative abundance ofAcinetobacterreached 70.8%. At the start of the granulation phase the relative abundance ofAgrobacteriumreached 35.9% and that ofDipodascus89.7% during the mature granule phase. Fluffy granules were detected on day 43. The granules with filamentous overgrowth were not stable and they lysed on day 46 resulting in biomass wash-out. It was found that the reactor operation strategy resulted in stable aerobic granules for 46 days. As the reactor operations remained the same from the mature granule phase to the end of the experiment, the disintegration of the granules after day 46 was due to changes in the microbial community structure and not by the reactor operation.

The amount of nanoparticles (NP), such as TiO2, has increased substantially in the environment. It is still largely unknown, however, how NP might interact with earthworms and organic material and how this might affect the bacterial community structure and their functionality. Therefore, an arable soil was amended with TiO2 NP at 0, 150 or 300 mg kg−1 and subjected to different treatments. Treatments were soil amended with ten earthworms (Eisenia fetida (Savigny, 1826)) with fully developed clitellum and an average fresh mass of 0.5 to 500 g dry soil, 1.75 g tyndallized Quaker® oat seeds Avena sativa (L.) kg−1, or earthworms plus oat seeds, or left unamended. The bacterial community structure was monitored throughout the incubation period. The bacterial community in the unamended soil changed over time and application of oats, earthworm and a combination of both even further, with the largest change found in the latter. Application of NP to the unamended soil and the earthworm-amended soil altered the bacterial community, but combining it by adding oats negated that effect. It was found that the application of organic material, that is, oats, reduced the effect of the NP applied to soil. However, as the organic material applied was mineralized by the soil microorganisms, the effect of NP increased again over time.

Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health.

Toxic compounds, such as 4-chlorophenol (4-CP), which is a common pollutant in wastewater, are removed efficiently from sequencing batch reactors (SBRs) by microorganisms. The bacterial community in aerobic granules formed during the removal of 4-CP in a SBR was monitored for 63days. The SBR reactor was operated with a constant filling and withdrawal time of 7 and 8min and decreasing settling time (30, 5, 3 and 2min) to induce the formation of aerobic granules. During the acclimation period lasting 15days (30min settling time) had a strong effect on the bacterial community. From day 18 onwards, Sphingobium and Comamonadaceae were detected. Rhizobiaceae were dominant from day 24 to day 28 when stable aerobic granules were formed. At day 35, fluffy granules were formed, but the bacterial community structure did not change, despite the changes in the reactor operation to inhibit filamentous bacteria growth. This is the first report on changes in the bacterial community structure of aerobic and fluffy granules during granulation process in a reactor fed with 4-CP and the prediction of its metabolic pathways.

In this study, the effect of deforestation and cultivation of maize (Zea mays L.) on the physicochemical characteristics and the bacterial community structure in soil were studied at the national park Area de Proteccion de Flora y Fauna Nevado de Toluca in Mexico. Soil was sampled from three forested areas in the national park, from three deforested areas grazed by animals and from three areas cultivated with maize. The soil was characterized chemically and biologically, whilst the bacterial community structure was investigated through 454 pyrosequencing of the 16S rRNA gene. The pH in the forest soil decreased from 6·1 to 5·3 in the maize-cultivated soil, whilst the soil organic C content decreased 1·4 times in the arable soil compared with the forest soil. The microbial biomass C decreased 2·9 times in the arable soil compared with the forest soil, but the metabolic quotient qCO2 (ratio basal respiration to microbial biomass C) nearly doubled. Deforestation and maize cultivation reduced the abundance of Proteobacteria, Actinobacteria and Bacteroidetes, whereas Acidobacteria, Chloroflexi, Gemmatimonadetes and Firmicutes were resistant to these changes. It was found that soil characteristics were affected negatively by deforestation and nearly half of the organic matter was lost, and on these sloped fields, erosion will be high, further decreasing soil fertility. Although the relative abundance of a number of bacterial groups was reduced by deforestation, others were not affected by land-use change. Copyright © 2014 John Wiley & Sons, Ltd.

Soil microbial biomass has been determined since the mid 1970's by the chloroform fumigation incubation technique as proposed by Jenkinson and Powlson (1976). The microbial biomass C can be determined by subtracting the CO2 emitted from an unfumigated soil (mineralization of soil organic matter) from that emitted from a chloroform fumigated inoculated soil (mineralization of soil organic matter and killed soil microorganisms) and dividing the difference by a proportionality factor (kC = 0.45). The question remained which microorganisms recolonized a fumigated soil. An arable soil was fumigated for one day with ethanol-free chloroform or left unfumigated and incubated aerobically after removal of the chloroform for 10 days. The bacterial population structures were determined in the fumigated and unfumigated soil after 0, 1, 5 and 10 days by means of 454 pyrosequencing of the 16S rRNA gene. Fumigating the arable soil reduced significantly the relative abundance of phylotypes belonging to different groups, but increased the relative abundance of only four genera belonging to two phyla (Actinobacteria and Firmicutes) and two orders (Actinomycetales and Bacillales). The relative abundance of phylotypes belonging to the Micromonospora (Micromonosporaceae) increased significantly from 0.2% in the unfumigated soil to 6.7% in the fumigated soil and that of Bacillus (Bacillaceae) from 3.6% to 40.8%, Cohnella (Paenibacillaceae) from undetectable amounts to 0.6% and Paenibacillus (Paenibacillaceae) from 0.3% to 4.2%. The relative percentage of phylotypes belonging to the Acidobacteria, Bacteroidetes, Chloroflexi, Gemmatimonadetes and Proteobacteria (α- β-, δ- and γ-Proteobacteria) were significantly lower in the fumigated than in the unfumigated soil and in most of them the relative abundance of different bacterial orders (i.e. Gp3, Gp4, Gp6, Sphingobacteriales, Gemmatimonadales, Rhodospirillales, Burkholderiales, Xanthomonadales) was reduced strongly (P

After chloroform fumigating an arable soil, the relative abundance of phylotypes belonging to only two phyla (Actinobacteria and Firmicutes) and two orders [Actinomycetales and Bacillales (mostly Bacillus)] increased in a subsequent aerobic incubation, while it decreased for a wide range of bacterial groups. It remained to be seen if similar bacterial groups were affected when an extreme alkaline saline soil was fumigated. Soil with electrolytic conductivity between 139 and 157 dS m−1, and pH 10.0 and 10.3 was fumigated and the bacterial community structure determined after 0, 1, 5 and 10 days by analysis of the 16S rRNA gene, while an unfumigated soil served as control. The relative abundance of the Firmicutes increased in the fumigated soil (52.8 %) compared to the unfumigated soil (34.2 %), while that of the Bacteroidetes decreased from 16.2 % in the unfumigated soil to 8.8 % in the fumigated soil. Fumigation increased the relative abundance of the genus Bacillus from 14.7 % in the unfumigated soil to 25.7 %. It was found that phylotypes belonging to the Firmicutes, mostly of the genus Bacillus, were dominant in colonizing the fumigated alkaline saline as found in the arable soil, while the relative abundance of a wide range of bacterial groups decreased.

In this study we analyzed the microbiota composition of fecal samples from the lesser-long nosed bat Leptonycteris yerbabuenae in different reproductive stages (juveniles and adult bats of both sexes as well as pregnant and lactating females). The V4 region of the 16s rRNA gene from 33 individuals was analyzed using alpha and beta diversity metrics. We found that microbiota diversity (expressed in Amplicon Sequence Variants) is higher in pregnant and lactating females. The microbiota of the juveniles and non-reproductive adults was dominated by Gammaproteobacteria and Firmicutes. Reproductive females had a much more diverse microbiota, with a significant increase in phyla such as Bacteroidetes and Alphaproteobacteria. There was no difference in fecal microbiota diversity between pregnant and lactating females and juveniles and non-reproductive adults. Results suggest that differences in microbiota diversity are related to reproduction. We infer that males maintain stable microbiota composition because they do not undergo the large physiological changes that females do during reproduction and maintain a more specialized diet throughout all life stages.

The alkaline α-amylase produced by Texcoconibacillus texcoconensis 13CC(T) strain was identified by random mutagenesis and confirmed by directed mutagenesis. A transposon mutagenesis approach was taken to identify the gene responsible for the degradation of starch in T. texcoconensis 13CC(T) strain. The deduced amino acids of the amy gene had a 99% similarity with those of Bacillus selenitireducens MLS10 and 97% with those of Paenibacillus curdlanolyticus YK9. The enzyme showed a maximum activity of 131.1 U/mL at 37 °C and pH 9.5 to 10.5. In situ activity of the enzyme determined by polyacrylamide gel electrophoresis showed only one band with amylolytic activity. This is the first report of a bacterium isolated from the extreme alkaline-saline soil of the former Lake Texcoco (Mexico) with amylolytic activity in alkaline conditions while its potential as a source of amylases for the industry is discussed.

In this study, the effect of limited tillage versus traditional tillage, residue retention versus removal and crop rotation (maize–wheat) versus monoculture (maize) on the bacterial community structure in soils was investigated by means of 454 pyrosequencing of the 16S rRNA gene. Using taxonomic and phylogenetic information it was found that zero tillage most affected the bacterial communities. The relative abundance of Actinobacteria, Betapreoteobacteria and Gammaproteobacteria was affected by tillage and correlated to the total organic carbon (TOC) and clay content in soil. Residue management had a significant effect on the bacterial community structure when phylogenetic membership and the total enumeration of bacteria were considered. Residue management affected the relative abundance of Bacteroidetes, Betaproteobacteria, Cyanobacteria and Gemmatimonadetes. When no tillage was applied, crop residue management affected the microbial communities more than when conventional tillage was applied. Wheat–maize rotation or crop monoculture did not affect the bacterial community structure. No significant differences in richness, diversity and total abundance of bacteria was found between the treatments. This indicated that even though phylotypes changed, the number and diversity of the bacterial communities were similar.

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 iron-oxidizing 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.

Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health.

Biodegradation of phenolic compounds in bioreactors is well documented, but the changes in the bacterial populations dynamics during degradation were not that often. A glass bubble column used as reactor was inoculated with activated sludge, spiked with 2-chlorophenol, phenol and m-cresol after 28 days and maintained for an additional 56 days, while the 16S rRNA gene from metagenomic DNA was monitored. Proteobacteria (68.1%) dominated the inoculum, but the bacterial composition changed rapidly. The relative abundance of Bacteroidetes and Firmicutes decreased from 4.8 and 9.4 to