The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR / A influência da escolha de iniciadores na filogenia de Archaea em ensaios de PCR para o gene rRNA 16S

Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

A amplificação de genes que codificam o rRNA 16S por reação em cadeia da polimerase (PCR) e o seu sub sequentesequenciamento consistem em uma ferramenta importante na caracterização de comunidades microbianas presentes em amostras ambientais. No entanto, apesar do crescente número de sequências de DNA de Archaea depositadas em bancos de dados, a especificidade e efetividade dos iniciadores de PCR descritos como universais e amplamente utilizados na descrição desse grupo ainda não está clara. Neste estudo foram comparados os perfis filogenéticos de comunidades de arqueias obtidos a partir amostras de DNA de sedimentos lacustres do Cerrado submetidas a ensaios de PCR empregando três pares de iniciadores específicos para Archaea, comumente utilizados neste tipo de estudo. Nossos resultados indicam que as comunidades de arqueias detectadas com cada par de iniciadores apresentaram grande variação filogenética, sugerindo que a escolha de iniciadores dirigidos ao gene de rRNA 16S tem efeito significativo no perfil da comunidade descrita, com diferenças tanto em relação aos táxons detectados, como nas estimativas de unidades taxonômicas operacionais (OTU).

The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR

Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

Resumo A amplificação de genes que codificam o rRNA 16S por reação em cadeia da polimerase (PCR) e o seu subsequente sequenciamento consistem em uma ferramenta importante na caracterização de comunidades microbianas presentes em amostras ambientais. No entanto, apesar do crescente número de sequências de DNA de Archaea depositadas em bancos de dados, a especificidade e efetividade dos iniciadores de PCR descritos como universais e amplamente utilizados na descrição desse grupo ainda não está clara. Neste estudo foram comparados os perfis filogenéticos de comunidades de arqueias obtidos a partir amostras de DNA de sedimentos lacustres do Cerrado submetidas a ensaios de PCR empregando três pares de iniciadores específicos para Archaea, comumente utilizados neste tipo de estudo. Nossos resultados indicam que as comunidades de arqueias detectadas com cada par de iniciadores apresentaram grande variação filogenética, sugerindo que a escolha de iniciadores dirigidos ao gene de rRNA 16S tem efeito significativo no perfil da comunidade descrita, com diferenças tanto em relação aos táxons detectados, como nas estimativas de unidades taxonômicas operacionais (OTU).

The influence of primer choice on archaeal phylogenetic analyses based on 16S rRNA gene PCR / A influência da escolha de iniciadores na filogenia de Archaea em ensaios de PCR para o gene rRNA 16S

Abstract Polymerase chain reaction (PCR) assays targeting 16S rRNA genes followed by DNA sequencing are still important tools to characterize microbial communities present in environmental samples. However, despite the crescent number of deposited archaeal DNA sequences in databases, until now we do not have a clear picture of the effectiveness and specificity of the universal primers widely used to describe archaeal communities from different natural habitats. Therefore, in this study, we compared the phylogenetic profile obtained when Cerrado lake sediment DNA samples were submitted to 16S rDNA PCR employing three Archaea-specific primer sets commonly used. Our findings reveal that specificity of primers differed depending on the source of the analyzed DNA. Furthermore, archaeal communities revealed by each primer pair varied greatly, indicating that 16S rRNA gene primer choice affects the community profile obtained, with differences in both taxon detection and operational taxonomic unit (OTU) estimates.

Resumo A amplificação de genes que codificam o rRNA 16S por reação em cadeia da polimerase (PCR) e o seu subsequente sequenciamento consistem em uma ferramenta importante na caracterização de comunidades microbianas presentes em amostras ambientais. No entanto, apesar do crescente número de sequências de DNA de Archaea depositadas em bancos de dados, a especificidade e efetividade dos iniciadores de PCR descritos como universais e amplamente utilizados na descrição desse grupo ainda não está clara. Neste estudo foram comparados os perfis filogenéticos de comunidades de arqueias obtidos a partir amostras de DNA de sedimentos lacustres do Cerrado submetidas a ensaios de PCR empregando três pares de iniciadores específicos para Archaea, comumente utilizados neste tipo de estudo. Nossos resultados indicam que as comunidades de arqueias detectadas com cada par de iniciadores apresentaram grande variação filogenética, sugerindo que a escolha de iniciadores dirigidos ao gene de rRNA 16S tem efeito significativo no perfil da comunidade descrita, com diferenças tanto em relação aos táxons detectados, como nas estimativas de unidades taxonômicas operacionais (OTU).

El papel del laboratorio de microbiología en la práctica clínica / The role of the microbiology laboratory in clinical practice

Los seres humanos albergamos en el cuerpo a cientos de miles de microbios (bacterias, virus, hongos, archaea). Con la mayoría convivimos armónicamente, y obtenemos beneficios mutuos. Ellos participan activamente en nuestros procesos metabólicos e inmunológicos, y nosotros les damos vivienda y nutrientes [1]. Si el equilibrio se altera, como ocurre cuando el sistema inmune se suprime, algunos de estos microorganismos aprovechan la oportunidad y desencadenan infección [2], siendo este el origen de la mayoría de las infecciones, pero no el único, pues los ambientes externos al cuerpo humano también están poblados de microbios, y si bien pocos se consideran patógenos, al entrar en contacto con ellos adquirimos infecciones que llamamos exógenas. De acuerdo con la Organización Mundial de la Salud (OMS), las enfermedades transmisibles están entre las 10 principales causas de muerte en el mundo, y excluyendo la infección por SARS-CoV-2 (COVID-19) en 2021, las infecciones respiratorias agudas fueron la cuarta causa más frecuente de defunción a nivel mundial [3]. El laboratorio de microbiología clínica tiene un papel crucial en el proceso diagnóstico, terapéutico y preventivo de las enfermedades infecciosas causadas por bacterias, hongos, virus y parásitos, pues determinar el agente causal de manera eficaz permite tomar acciones oportunas para definir el manejo individual de las personas infectadas y cortar la cadena de transmisión cuando se requiera [2]

Expression and characterization of a bifunctional thermal β-glucosidase IuBgl3 from thermophilic archaeon Infirmifilum uzonense / 生物工程学报

β-glucosidase has important applications in food, medicine, biomass conversion and other fields. Therefore, exploring β-glucosidase with strong stability and excellent properties is a research hotspot. In this study, a GH3 family β-glucosidase gene named Iubgl3 was successfully cloned from Infirmifilum uzonense. Sequence analysis showed that the full length of Iubgl3 was 2 106 bp, encoding 702 amino acids, with a theoretical molecular weight of 77.0 kDa. The gene was cloned and expressed in E. coli and the enzymatic properties of purified IuBgl3 were studied. The results showed that the optimal pH and temperature for pNPG hydrolysis were 5.0 and 85 ℃, respectively. The enzyme has good thermal stability, and more than 85% of enzyme activity can be retained after being treated at 80 ℃ for2 h. This enzyme has good pH stability and more than 85% of its activity can be retained after being treated at pH 4.0-11.0 for 1 h. It was found that the enzyme had high hydrolysis ability to p-nitrophenyl β-d-glucoside (pNPG) and p-nitrophenyl β-d-xylopyranoside (pNPX). When pNPG was used as the substrate, the kinetic parameters Km and Vmax were 0.38 mmol and 248.55 μmol/(mg·min), respectively, and the catalytic efficiency kcat/Km was 6 149.20 s-1mmol-1. Most metal ions had no significant effect on the enzyme activity of IuBgl3. SDS completely inactivated the enzyme, while EDTA increased the enzyme activity by 30%. This study expanded the β-glucosidase gene diversity of the thermophilic archaea GH3 family and obtained a thermostable acid bifunctional enzyme with good industrial application potential.

Enhanced heterologous expression of the cytochrome c from uncultured anaerobic methanotrophic archaea / 生物工程学报

Cytochrome c is a type of heme proteins that are widely distributed in living organisms. It consists of heme and apocytochrome c, and has potential applications in bioelectronics, biomedicine and pollutant degradation. However, heterologous overexpression of cytochrome c is still challenging. To date, expression of the cytochrome c from uncultured anaerobic methanotrophic archaea has not been reported, and nothing is known about the function of this cytochrome c. A his tagged cytochrome c was successfully expressed in E. coli by introducing a thrombin at the N-terminus of CytC4 and co-expressing CcmABCDEFGH, which is responsible for the maturation of cytochrome c. Shewanella oneidensis, which naturally has enzymes for cytochrome c maturation, was then used as a host to further increase the expression of CytC4. Indeed, a significantly higher expression of CytC4 was achieved in S. oneidensis when compared with in E. coli. The successful heterologous overexpression of CytC4 will facilitate the exploitation of its physiological functions and biotechnological applications.

Ligands of TetR family transcriptional regulators: a review / 生物工程学报

TetR family transcriptional regulators (TFRs) are widely distributed in bacteria and archaea, and the first discovered TFR was confirmed to control the expression of tetracycline efflux pump in Escherichia coli. TFRs can bind DNAs and ligands. Small molecule ligands can induce conformational changes of TFRs, inhibiting or promoting TFRs to control target gene expression. Currently, TFRs have a wide variety of ligands, including carbohydrates, proteins, fatty acids and their derivatives, metal ions, and so on. Due to the diversity of ligands, TFRs regulate a wide range of physiological processes, from basic carbon metabolism and nitrogen metabolism to quorum sensing and antibiotic biosynthesis. On the basis of the recent studies in our laboratory and the literature, we review here the regulatory mechanism mediated by ligands of TFRs in primary and secondary metabolism, as well as the application of ligands for TFRs in the development of gene route and the activation of antibiotic biosynthesis.

Comparison of intestinal microbial community succession based on different universal primer sets / 生物工程学报

The important role of intestinal microorganisms in human health has been widely confirmed. At present, most of the studies on intestinal microorganisms are based on amplification of the V3-V4 region of bacterial 16S rRNA gene, and little attention has been paid to archaea. In this study, a primer set which can amplify 16S rRNA gene of both bacteria and archaea at the same time was used. By comparing the community changes before and after probiotics intake, it showed that this primer set is suitable for analyzing the changes of human intestinal bacteria and archaea communities. The fecal samples of volunteers were collected, and the amplification and high-throughput sequencing were carried out by using bacterial primer set (B primer) and bacterial and archaeal universal primer (AB primer); several commonly used rRNA databases were used to determine the amplification ability of the primer set to bacteria and archaea. The results showed that AB primer could display the bacterial community amplified by B primer, and could obtain the sequence of common methanogenic archaea in intestinal tract. AB primer set can analyze the bacteria and archaea in the intestinal tract at the same time by only one amplification and sequencing, which can show the structure of intestinal microbial community more comprehensively, which is suitable for the research of intestinal microorganisms.

The effect of introduction of chicken manure on the biodiversity and performance of an anaerobic digester

Background: Ammonium stress is a prime limiting phenomenon that occurs during methane formation from poultry manure. It is caused by elevated ammonium nitrogen concentrations that result from substrate decomposition. The amounts of methane formed depend on the activity of methanogenic microbes. Results: During the research reported in this paper, the response of a mesophilic consortium inhabiting a biogas reactor to rising load of poultry manure was investigated. The taxonomic composition of bacterial population was mostly typical, however syntrophic bacteria were not detected. This absence resulted in limitation of succession of some methanogenic microorganisms, especially obligate hydrogenotrophs. The methanogenic activity of the consortium was totally dependent on the activity of Methanosaeta. Inhibition of methanoganesis was noticed at ammonium nitrogen concentration of 3.68 g/L, total cessation occurred at 5.45 g/L. Significant amounts of acetic acid in the fermentation pulp accompanied the inhibition. Conclusions: The effectiveness of the consortium was totally dependent on the metabolic activity of the acetoclastic Methanoseata genus and lack of SAOB did not allow hydrogenotrophic methanogens to propagate and lead to cessation of biogas production at an elevated ammonium concentration at which acetoclastic methanogens were inhibited.

Correlación entre los microorganismos oxidantes del amonio y los factores ambientales durante el compostaje de estiércol de ganado / Correlation between ammonia-oxidizing microorganisms and environmental factors during cattle manure composting

Abstract Cattle manure composting was performed in an aerated vessel. Community structure and diversity of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated using polymerase chain reaction and denaturing gradient gel electrophoresis (PCR-DGGE) techniques targeting the ammonia monooxygenase alpha subunit (amoA) gene and the correlation between AOB and AOA communities and environmental factors was explored. Thirteen (13) AOB sequences were obtained, which were closely related to Nitrosomonas spp., Nitrosomonas eutropha, and Nitrosospira spp. and uncultured bacteria, among which Nitrosomonas spp. were predominant. Excessively high temperature and high ammonium concentration were not favorable for AOB growth. Five AOA sequences, belonging to Candidatus Nitrososphaera gargensis and to an uncultured archaeon, were obtained. During composting, community diversity of AOB and AOA fluctuated, with AOA showing a higher Shannon-Wiener index. The AOB community changed more dramatically in the mesophilic stage and the early thermophilic stage, whereas the most obvious AOA community succession occurred in the late thermophilic stage, the cooling stage and the maturity stage. Water content, total nitrogen (TN) and ammonium concentration were more relevant to the AOB community structure, while higher correlations were observed between ammonia, nitrate and TN and the AOA community. AOB community diversity was negatively correlated with pH (r = -0.938, p < 0.01) and water content (r = -0.765, p < 0.05), while positively correlated with TN (r = 0.894, p < 0.01). AOA community diversity was negatively correlated with ammonium concentration (r = -0.901, p < 0.01). Ammonium concentration played an important role in the succession of AOB and AOA communities during composting.

Resumen Se llevó a cabo un compostaje de estiércol de ganado en un recipiente aireado. Se investigó la estructura de la comunidad y la diversidad de bacterias oxidantes del amoníaco (AOB) y las arqueas oxidantes del amoníaco (AOA) mediante el uso de las técnicas de reacción en cadena de la polimerasa y la electroforesis en gel con gradiente de desnaturalización (PCR-DGGE) dirigidas al gen de la subunidad alfa de la amonio monooxigenasa (amoA), y se exploró la correlación entre las comunidades AOB, AOA y los factores ambientales. Se obtuvieron 13 secuencias de AOB, las cuales se relacionaron estrechamente con Nitrosomonas spp., Nitrosomonas eutropha y Nitrosospira spp., y bacterias no cultivadas, entre las cuales fueron predominantes las Nitrosomonas spp. La temperatura excesivamente alta y la concentración de amonio elevada no fueron favorables para el crecimiento de las AOB. Se obtuvieron 5 secuencias de AOA, pertenecientes a Candidatus Nitrososphaera gargensis y un Archaeon no cultivado. Durante el compostaje, la diversidad de AOB y AOA fluctuó y las AOA mostraron un índice de Shannon-Wiener más alto. La comunidad de AOB cambió significativamente en la etapa mesofílica y la etapa termofílica temprana, mientras que la sucesión más obvia de la comunidad AOA ocurrió en la etapa termofílica tardía y las etapas de enfriamiento y de maduración. El contenido de agua, el nitrógeno total (TN) y la concentración de amonio fueron más relevantes para la estructura de la comunidad AOB, mientras que se observaron correlaciones mayores entre amoníaco, nitrato y TN, y la comunidad AOA. La diversidad de la comunidad AOB se correlacionó negativamente con el pH (r= -0,938; p < 0,01) y el contenido de agua (r = -0,765; p < 0,05), mientras que se relacionó positivamente con TN (r = 0,894; p < 0,01). La diversidad de la comunidad AOA se correlacionó negativamente con la concentración de amonio (r = -0,901; p < 0,01). La concentración de amonio desempenó un papel importante en la sucesión de las comunidades AOB y AOA durante el compostaje.

Evaluation of triclosan toxic effects on the methanogenic activity

BACKGROUND: Triclosan (TCS) is an antimicrobial agent widely used in health care and consumer products. This compound is present in sludge of wastewater treatment plants (WWTPs), and because of its bactericidal characteristics, it can inhibit the methanogenic activity in anaerobic digestion (AD) technology. The aim of this study was to evaluate the toxic effects of TCS on the methanogenic activity. RESULTS: Batch anaerobic reactors were used with TCS concentrations of 7.8, 15.7, 23.5, and 31.4 mg/L. These assays consisted in three successive feedings (I, II, and III), wherein the sludge was exposed to each TCS concentration and volatile fatty acid (VFA) substrate. For evaluation of the residual sludge activity during feeding III, only VFA was used. The results showed that the increase in TCS concentrations correlated with the reduction in methane (CH4) production. In this case, the minimum values were achieved for TCS concentration of 31.4 mg/L with CH4 levels between 101.9 and 245.3 during feedings I, II, and III. Regarding the effect of TCS on VFA consumption, an inhibitory effect was detected for TCS concentrations of 23.5 and 31.4 mg/L, with concentrations of acetic, butyric, and propionic acids at the end of the assay (37 d) between 153.6 and 206.8, 62.5 and 60.1, and 93.4 and 110 mg/L, respectively. Regarding the removal of TCS during AD, these values were above 47%. Conclusion: TCS is an inhibitor of methanogenic activity with a decrease between 63 and 70% during the different feedings. The CH4 production was not recovered during feeding III, with inhibition percentages of 21­72%.

Ectopic expression of archaeal TRAM-encoding genes in rice improves its drought-tolerance / 生物工程学报

Drought stress affects the growth and development of rice, resulting in severe loss in yield and quality. Ectopic expression of the bacterial RNA chaperone, cold shock protein (Csp), can improve rice drought tolerance. Archaeal TRAM (TRM2 and MiaB) proteins have similar structure and biochemical functions as bacterial Csp. Moreover, DNA replication, transcription and translation of archaea are more similar to those in eukaryotes. To test if archaeal RNA chaperones could confer plant drought tolerance, we selected two TRAM proteins, Mpsy_3066 and Mpsy_0643, from a cold-adaptive methanogenic archaea Methanolobus psychrophilus R15 to study. We overexpressed the TRAM proteins in rice and performed drought treatment at seedling and adult stage. The results showed that overexpression both TRAM proteins could significantly improve the tolerance of rice to drought stress. We further demonstrated in rice protoplasts that the TRAMs could abolish misfolded RNA secondary structure and improve translation efficiency, which might explain how TRAMs improve drought tolerance transgenic rice. Our work supports that ectopic expression of archaeal TRAMs effectively improve drought tolerance in rice.

Exploring tRNA gene cluster in archaea

BACKGROUND Shared traits between prokaryotes and eukaryotes are helpful in the understanding of the tree of life evolution. In bacteria and eukaryotes, it has been shown a particular organisation of tRNA genes as clusters, but this trait has not been explored in the archaea domain. OBJECTIVE Explore the occurrence of tRNA gene clusters in archaea. METHODS In-silico analyses of complete and draft archaeal genomes based on tRNA gene isotype and synteny, tRNA gene cluster content and mobilome elements. FINDINGS We demonstrated the prevalence of tRNA gene clusters in archaea. tRNA gene clusters, composed of archaeal-type tRNAs, were identified in two Archaea class, Halobacteria and Methanobacteria from Euryarchaeota supergroup. Genomic analyses also revealed evidence of the association between tRNA gene clusters to mobile genetic elements and intra-domain horizontal gene transfer. MAIN CONCLUSIONS tRNA gene cluster occurs in the three domains of life, suggesting a role of this type of tRNA gene organisation in the biology of the living organisms.

Rendimiento de polihidroxialcanoatos (PHA) en microorganismos halófilos aislados de salinas / Polyhydroxyalkanoates (PHA) performance of halophilic microorganisms isolated from salty lagoon

En este trabajo se determinó el rendimiento de polihidroxialcanoatos (PHA) producido por microorganismos aislados de suelo y aguas de las salinas de Morrope, Lambayeque, Perú. La población de microorganismos se enriqueció con caldo HM1, con glucosa (15 gL-1) como fuente de carbono, modificado con 15, 20 y 25 g/100 mL de NaCl, se incubó a 30 °C en aerobiosis hasta observar turbidez o película por el crecimiento se aisló en agar HM1 obteniendo cultivos de microorganismos halófilos. En caldo HM2 con glucosa (30 gL-1), con su respectiva concentración de NaCl se investigó la producción de gránulos de PHA y se determinó el tiempo requerido para observar el mayor número de células con gránulos de PHA. Los 20 cultivos con mayor número de células con gránulos se llevaron a fermentación a caldo HM2, cuantificándose la biomasa y PHA. La naturaleza del polímero y cálculo del rendimiento se realizó con cinco aislados microbianos correspondientes a la mayor concentración de NaCl, el mayor número de celular con gránulos en el menor tiempo. Se obtuvieron 234 aislados de microorganismos y en el 38.74% se observó gránulos de PHA mediante la tinción de Sudan Negro B, seleccionándose 20 cultivos de microorganismos con 40 a 85 células con gránulos de PHA. La biomasa osciló entre 0.005 a las 72 horas y 3.211 gL-1 a las 240 horas. El rendimiento p/x fue de 0.270 a 0.725 gg-1, destacando con más de 60% los microorganismos AE222 (60.73%), AE2019 (63.10%) y AE228 (72.52%). Estos microorganismos son considerados promisorios para la producción de PHA.

In this work, we determine the polyhydroxyalkanoates (PHA) yield of microorganisms of soil and water from salty lagoons of Morrope, Lambayeque, Peru. Microorganisms were enriched in modified HM1 broth with 15, 20 and 25 g/100 mL of NaCl, incubated at 30 °C in aerobiosis. After observed turbidity or film, aliquots were taken and seeded on HM1 agar obtaining 234 bacterial isolates that by lipophilic Sudan Negro B staining were observed the presence of 93 bacterial isolates with PHA granules, which were cultured in HM² broth with their respective concentrations of NaCl for 144 hours, quantifying a range of 4-85 cells with granules in five microscopic fields observed, selecting 20 bacterial isolates with the presence of 40-85 cells with granules, then they were taken to fermentation where the optimal incubation time was determined, where the cells are clearly differentiated with PHA granules. To determine the nature of the polymer produced, five bacterial isolates corresponding to the culture with the highest concentration of NaCl and the highest number of cells with PHA granules with the shortest growth time, but not necessarily the highest biomass, were selected, these reached 0.500; 0.300; 0.167; 0.183 and 0.417 gL-1 of PHA, with 1.850; 0.522; 0.275; 0.290 and 0.575 gL-1 of biomass and 0.270; 0.575; 0.607; 0.631 and 0.725 gg-1 yield Y (p/x). The highest yield was 72.52% of cellular mass in PHA being considered a promising and profitable performance for the extraction of the polymer.

Polyphyly in 16S rRNA-based LVTree Versus Monophyly in Whole-genome-based CVTree / 基因组蛋白质组与生物信息学报·英文版

We report an important but long-overlooked manifestation of low-resolution power of 16S rRNA sequence analysis at the species level, namely, in 16S rRNA-based phylogenetic trees polyphyletic placements of closely-related species are abundant compared to those in genome-based phylogeny. This phenomenon makes the demarcation of genera within many families ambiguous in the 16S rRNA-based taxonomy. In this study, we reconstructed phylogenetic relationship for more than ten thousand prokaryote genomes using the CVTree method, which is based on whole-genome information. And many such genera, which are polyphyletic in 16S rRNA-based trees, are well resolved as monophyletic clusters by CVTree. We believe that with genome sequencing of prokaryotes becoming a commonplace, genome-based phylogeny is doomed to play a definitive role in the construction of a natural and objective taxonomy.

Biotechnological applications of archaeal enzymes from extreme environments

To date, many industrial processes are performed using chemical compounds, which are harmful to nature. An alternative to overcome this problem is biocatalysis, which uses whole cells or enzymes to carry out chemical reactions in an environmentally friendly manner. Enzymes can be used as biocatalyst in food and feed, pharmaceutical, textile, detergent and beverage industries, among others. Since industrial processes require harsh reaction conditions to be performed, these enzymes must possess several characteristics that make them suitable for this purpose. Currently the best option is to use enzymes from extremophilic microorganisms, particularly archaea because of their special characteristics, such as stability to elevated temperatures, extremes of pH, organic solvents, and high ionic strength. Extremozymes, are being used in biotechnological industry and improved through modern technologies, such as protein engineering for best performance. Despite the wide distribution of archaea, exist only few reports about these microorganisms isolated from Antarctica and very little is known about thermophilic or hyperthermophilic archaeal enzymes particularly from Antarctica. This review summarizes current knowledge of archaeal enzymes with biotechnological applications, including two extremozymes from Antarctic archaea with potential industrial use, which are being studied in our laboratory. Both enzymes have been discovered through conventional screening and genome sequencing, respectively.

Draft genome sequence of sulfur-reducing archaeon Thermococcus thioreducens DSM 14981T

Abstract Thermococcus thioreducens DSM 14981T, a sulfur-reducing archaeon, was isolated from the rainbow hydrothermal vent site on the Mid-Atlantic Ridge. Herein, we report the draft genome sequence of T. thioreducens DSM 14981T; we obtained 41 contigs with a genome size of 2,052,483 bp and G + C content of 53.5%. This genome sequence will not only help understand how the archaeon adapts to the deep-sea hydrothermal environment but also aid the development of enzymes that are highly stable under extreme conditions for industrial applications.

Characterization of a hyperthermophilic sulphur-oxidizing biofilm produced by archaea isolated from a hot spring

Background: Sulphur-oxidizing microorganisms are widely used in the biofiltration of total reduced sulphur compounds (odorous and neurotoxic) produced by industries such as the cellulose and petrochemical industries, which include high-temperature process steps. Some hyperthermophilic microorganisms have the capability to oxidize these compounds at high temperatures (N60°C), and archaea of this group, for example, Sulfolobus metallicus, are commonly used in biofiltration technology. Results: In this study, a hyperthermophilic sulphur-oxidizing strain of archaea was isolated from a hot spring (Chillán, Chile) and designated as M1. It was identified as archaea of the genus Sulfolobus (99% homology with S. solfataricus 16S rDNA). Biofilms of this culture grown on polyethylene rings showed an elemental sulphur oxidation rate of 95.15 ± 15.39 mg S l-1 d-1, higher than the rate exhibited by the biofilm of the sulphur-oxidizing archaea S. metallicus (56.8 ± 10.91 mg l-1 d-1). Conclusions: The results suggest that the culture M1 is useful for the biofiltration of total reduced sulphur gases at high temperatures and for other biotechnological applications.

Comparative Analysis of Predicted Gene Expression among Crenarchaeal Genomes

Research into new methods for identifying highly expressed genes in anonymous genome sequences has been going on for more than 15 years. We presented here an alternative approach based on modified score of relative codon usage bias to identify highly expressed genes in crenarchaeal genomes. The proposed algorithm relies exclusively on sequence features for identifying the highly expressed genes. In this study, a comparative analysis of predicted highly expressed genes in five crenarchaeal genomes was performed using the score of Modified Relative Codon Bias Strength (MRCBS) as a numerical estimator of gene expression level. We found a systematic strong correlation between Codon Adaptation Index and MRCBS. Additionally, MRCBS correlated well with other expression measures. Our study indicates that MRCBS can consistently capture the highly expressed genes.

Anaerobic microbiota: spatial-temporal changes in the sediment of a tropical coastal lagoon with ephemeral inlet in the Gulf of Mexico / Microbiota anaerobia: cambios espacio-temporales en el sedimento de una laguna costera tropical con boca efímera en el Golfo de México

Abstract:Sulfate-reducing bacteria (SRB) and methanogenic archaea (MA) share common niches in coastal sediments during the terminal phases of the anaerobic mineralization of organic matter. The purpose of this study was to analyze the spatial - temporal variation of SRB and MA in the sediments of a tropical coastal lagoon with ephemeral inlet (La Mancha, Veracruz, Gulf of Mexico) and its relationship with environmental changes. A total of 24 sediment samples were collected during the dry (April, May), rainy (July, September) and Northern (November, February) seasons in the period 2013-2014. Microbiological analyses included the quantification of the viable SRB and MA with different substrates, as well as mineralization experiments to determine the effect of sulfate on acetate oxidation. The analyzed environmental variables in the sediments included: temperature, pH, Eh, salinity, sulfates, H2S, volatile solids, carbohydrates, and granulometric characteristics. Major changes occurred between the dry and rainy seasons. During the dry season, sulfate-reducing abundance was significantly greater with lactate (8.3x105 - 1.2x107 cells / g) and propionate (1.8x105 - 6.6x106 cells / g) as substrates, while the MA that use methanol were dominant (4.2x105 - 9.1x106 cells / g). In contrast, during the rainy season, hydrogenophylic (2.6x105 - 8.3x106 cells/g) and acetoclastic (5.4x105-6.4x106 cells / g) MA increased significantly and SRB decreased in the analyzed substrates. An apparent competition for acetate was observed, with a greater oxidation in the media with sulfates in the dry season (0.06 mM acetate / g sediment / day), and a greater oxidation in the media without sulfates in the rainy season (0.02 mM acetate / g sediment / day). SRB and MA were present throughout the sediment column, however SRB dominated in the first centimeters of the sediment while MA were abundant in deeper layers. In conclusion, SRB and MA together played a role in the mineralization of organic matter in the sediments of La Mancha lagoon, with sulfate-reduction dominating in the dry season (closed inlet) and methanogenesis during the rainy season (open inlet). Changes in rainfall and river input in this lagoon significantly affect salinity and sulfate content, the main factors that regulate the dynamics of SRB and MA in the sediments. Rev. Biol. Trop. 64 (4): 1759-1770. Epub 2016 December 01.

Resumen:Las bacterias sulfatorreductoras (BSR) y las arqueas metanogénicas (AM) comparten nichos comunes en los sedimentos costeros durante las fases terminales de la mineralización anaerobia de la materia orgánica. El objetivo del presente estudio fue analizar la variación espacio-temporal de las BSR y AM en los sedimentos de una laguna costera tropical con una boca efímera (La Mancha, Veracruz, Golfo de México) y su relación con los cambios ambientales. Un total de 24 muestras de sedimentos fueron recolectadas en las temporadas de secas (abril, mayo), lluvias (julio, septiembre) y nortes (noviembre, febrero) en el periodo 2013 - 2014. Los análisis microbiológicos incluyeron la cuantificación de las BSR y AM viables con diferentes sustratos, así como experimentos de mineralización para determinar el efecto de los sulfatos en la oxidación del acetato. Las variables ambientales analizadas en los sedimentos incluyeron la temperatura, pH, Eh, salinidad, sulfatos, H2S, sólidos volátiles, carbohidratos y las características granulométricas. Los principales cambios se presentaron entre las estaciones de secas y lluvias. En la temporada de secas la abundancia sulfatorreductora fue significativamente superior con lactato (8.3x105 - 1.2x107 células / g) y propionato (1.8x105 - 6.6x106 células / g) como sustratos, mientras que las AM que emplean metanol dominaron (4.2x105 - 9.1x106 células / g). Por el contrario, en la época de lluvias aumentaron significativamente las AM hidrogenofílicas (2.6x105-8.3x106 células / g) y acetoclásticas (5.4x105-6.4x106 células / g), disminuyendo las BSR con los sustratos analizados. Se determinó una competencia aparente por el acetato. Su oxidación fue mayor en los medios con presencia de sulfatos en las temporadas de secas (0.06 mM acetato / g sedimento / día), mientras que aumentó en los medios sin sulfatos en la época de lluvias (0.02 mM acetato / g sedimento / día). Las BSR y las AM estuvieron presentes a lo largo de la columna sedimentaria; sin embargo, las BSR dominaron en los primeros centímetros del sedimento y las AM abundaron a mayor profundidad. En conclusión las BSR y AM participaron de manera conjunta en la mineralización de la materia orgánica en los sedimentos de la laguna de La Mancha, dominando la sulfatorreducción en la temporada de secas (boca cerrada) y la metanogénesis en la época de lluvias (boca abierta). Los cambios en el aporte fluvial y la precipitación en esta laguna afectaron significativamente la salinidad y el contenido de sulfatos, siendo los principales factores que regularon la dinámica de las BSR y AM en los sedimentos.