Archaeal Communities in a Heterogeneous Hypersaline-Alkaline Soil.

In this study the archaeal communities in extreme saline-alkaline soils of the former lake Texcoco, Mexico, with electrolytic conductivities (EC) ranging from 0.7 to 157.2 dS/m and pH from 8.5 to 10.5 were explored. Archaeal communities in the 0.7 dS/m pH 8.5 soil had the lowest alpha diversity values and were dominated by a limited number of phylotypes belonging to the mesophilic Candidatus Nitrososphaera. Diversity and species richness were higher in the soils with EC between 9.0 and 157.2 dS/m. The majority of OTUs detected in the hypersaline soil were members of the Halobacteriaceae family. Novel phylogenetic branches in the Halobacteriales class were detected in the soil, and more abundantly in soil with the higher pH (10.5), indicating that unknown and uncharacterized Archaea can be found in this soil. Thirteen different genera of the Halobacteriaceae family were identified and were distributed differently between the soils. Halobiforma, Halostagnicola, Haloterrigena, and Natronomonas were found in all soil samples. Methanogenic archaea were found only in soil with pH between 10.0 and 10.3. Retrieved methanogenic archaea belonged to the Methanosarcinales and Methanomicrobiales orders. The comparison of the archaeal community structures considering phylogenetic information (UniFrac distances) clearly clustered the communities by pH.

Changes in methane oxidation activity and methanotrophic community composition in saline alkaline soils.

The soil of the former Lake Texcoco is a saline alkaline environment where anthropogenic drainage in some areas has reduced salt content and pH. Potential methane (CH4) consumption rates were measured in three soils of the former Lake Texcoco with different electrolytic conductivity (EC) and pH, i.e. Tex-S1 a >18 years drained soil (EC 0.7 dS m(-1), pH 8.5), Tex-S2 drained for ~10 years (EC 9.0 dS m(-1), pH 10.3) and the undrained Tex-S3 (EC 84.8 dS m(-1), pH 10.3). An arable soil from Alcholoya (EC 0.7 dS m(-1), pH 6.7), located nearby Lake Texcoco was used as control. Methane oxidation in the soil Tex-S1 (lowest EC and pH) was similar to that in the arable soil from Alcholoya (32.5 and 34.7 mg CH4 kg(-1) dry soil day(-1), respectively). Meanwhile, in soils Tex-S2 and Tex-S3, the potential CH4 oxidation rates were only 15.0 and 12.8 mg CH4 kg(-1) dry soil day(-1), respectively. Differences in CH4 oxidation were also related to changes in the methane-oxidizing communities in these soils. Sequence analysis of pmoA gene showed that soils differed in the identity and number of methanotrophic phylotypes. The Alcholoya soil and Tex-S1 contained phylotypes grouped within the upland soil cluster gamma and the Jasper Ridge, California JR-2 clade. In soil Tex-S3, a phylotype related to Methylomicrobium alcaliphilum was detected.

Isolation and phylogenic identification of soil haloalkaliphilic strains in the former Texcoco Lake.

A wide diversity of organisms exists in soil. Well-adapted groups can be found in extreme environments. A great economic and metabolic potential for extremozymes produced by organisms living at extreme environments has been reported. Extreme characteristics such as high salt content and high pH level make the soil of the former Texcoco Lake a unique place which has not been exploited. Therefore, in this study, 66 strains from soil of the former Texcoco Lake were isolated and phylogenetically analyzed using universal oligonucleotide primers. Different genera such as Kocuria, Micrococcus, Nesterenkonia, Halomonas, Salinicoccus, Kurthia, Gracilibacillus, and Bacillus were found. However, only 22 from all isolated strains were identified at specie level.

The bacterial community structure in an alkaline saline soil spiked with anthracene

Background: The application of polycyclic aromatic hydrocarbons (PAHs) will affect the bacterial community structure as some groups will be favoured and others not. An alkaline saline soil with electrolytic conductivity (EC) 56 dS m-1 was spiked with anthracene and acetone while their effect on bacterial community structure was investigated. Results: The percentages of Acidobacteria and Actinobacteria decreased over time, while the percentage of Proteobacteria, mostly Xanthomonadales, increased. The percentage of the phylotypes belonging to the Nocardioides, Rhodococcus and Streptomyces, known degraders of PAHs, was larger in the anthracene-amended soil than in the acetone-amended and unamended soil at day 14. The phylotypes belonging to the genera Sphingomonas, also a known degrader of PAHs, however, was lower. Weighted and unweighted PCoA with UniFrac indicated that phylotypes were similar in the different treatments at day 0, but changed at day 1. After 14 days, phylotypes in the unamended and acetone-amended soil were similar, but different from those in the anthracene-spiked soil. Conclusions: It was found that incubating the soil and contaminating it with anthracene changed the bacterial community structure, but spiking the soil with acetone had little or no effect on the bacterial community structure compared to the unamended soil.

Texcoconibacillus texcoconensis gen. nov., sp. nov., alkalophilic and halotolerant bacteria isolated from soil of the former lake Texcoco (Mexico).

A novel Gram-positive, rod-shaped, spore-forming bacterium, designated 13CC(T) was isolated from soil of the former lake Texcoco. The strain was aerobic, catalase-positive and oxidase-negative. It grew at salinities of 0-26% (w/v) NaCl with an optimum at 9-16% (w/v) NaCl. The cells contain peptidoglycan type A1γ, A1γ' with glycine instead of l-alanine and three variations of peptidoglycan type A4γ. The only quinone detected was MK-7. The major fatty acid was anteiso-C(15:0). The polar lipids fraction consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and three different phospholipids. The DNA G+C content was 37.5 mol%. Maximum-likelihood phylogenetic analysis based on 16S rRNA gene sequences revealed that strain 13CC(T) was closely related to members of the genus Bacillus and shared 92.35% similarity with Bacillus agaradhaerens, 92.28% with Bacillus neizhouensis and 92.21% with Bacillus locisalis. It is proposed based on the phenotypic, genotypic and phylogenetic analyses that the novel isolate should be classified as a representative of a new genus and novel species, for which the name Texcoconibacillus texcoconensis gen. nov., sp. nov. is proposed. The type strain of Texcoconibacillus texcoconensis is 13CC(T) ( =JCM 17654(T) =DSM 24696(T)).

Natronorubrum texcoconense sp. nov., a haloalkaliphilic archaeon isolated from soil of the former lake Texcoco (Mexico).

A new haloalkaliphilic archaeon, strain B4(T), was isolated from the former lake Texcoco in Mexico. The cells were Gram-negative, pleomorphic-shaped, pink to red pigmented and aerobic. Strain B4(T) required at least 2.5 M NaCl for growth, with optimum growth at 3.4 M NaCl. It was able to grow over a pH range of 7.5-10.0 and temperature of 25-50 °C, with optimal growth at pH 9 and 37 °C. Cells are lysed in hypotonic treatment with less than 1.3 M NaCl. The major polar lipids of strain B4(T) were phosphatidylglycerol and methyl-phosphatidylglycerophosphate. Phospholipids were detected, but not glycolipids. The nucleotide sequence of the 16S rRNA gene revealed that the strain B4(T) was phylogenetically related to members of the genus Natronorubrum. Sequence similarity with Natronorubrum tibetense was 96.28 %, with Natronorubrum sulfidifaciens 95.06 % and Natronorubrum sediminis 94.98 %. The G+C content of the DNA was 63.3 mol%. The name of Natronorubrum texcoconense sp. nov. is proposed. The type strain is B4(T) (=CECT 8067(T) = JCM 17497(T)).

Haloarchaeal assimilatory nitrate-reducing communities from a saline alkaline soil.

Assimilatory nitrate reduction (ANR) is a pathway wherein NO(3)(-) is reduced to NH(4)(+), an N species that can be incorporated into the biomass. There is little information about the ANR genes in Archaea and most of the known information has been obtained from cultivable species. In this study, the diversity of the haloarchaeal assimilatory nitrate-reducing community was studied in an extreme saline alkaline soil of the former lake Texcoco (Mexico). Genes coding for the assimilatory nitrate reductase (narB) and the assimilatory nitrite reductase (nirA) were used as functional markers. Primers to amplify and detect partial narB and nirA were designed. The analysis of these amplicons by cloning and sequencing showed that the deduced protein fragments shared >45% identity with other NarB and NirA proteins from Euryarchaeota and <38% identity with other nitrate reductases from Bacteria and Crenarchaeota. Furthermore, these clone sequences were clustered within the class Halobacteria with strong support values in both constructed dendrograms, confirming that desired PCR products were obtained. The metabolic capacity to assimilate nitrate by these haloarchaea seems to be important given that at pH 10 and higher, NH(4)(+) is mostly converted to toxic and volatile NH(3), and NO(3)(-) becomes the preferable N source.

Changes in the bacterial populations of the highly alkaline saline soil of the former lake Texcoco (Mexico) following flooding.

Flooding an extreme alkaline-saline soil decreased alkalinity and salinity, which will change the bacterial populations. Bacterial 16S rDNA libraries were generated of three soils with different electrolytic conductivity (EC), i.e. soil with EC 1.7 dS m(-1) and pH 7.80 (LOW soil), with EC 56 dS m(-1) and pH 10.11 (MEDIUM soil) and with EC 159 dS m(-1) and pH 10.02 (HIGH soil), using universal bacterial oligonucleotide primers, and 463 clone 16S rDNA sequences were analyzed phylogenetically. Library proportions and clone identification of the phyla Proteobacteria, Actinobacteria, Acidobacteria, Cyanobacteria, Bacteroidetes, Firmicutes and Cloroflexi showed that the bacterial communities were different. Species and genera of the Rhizobiales, Rhodobacterales and Xanthomonadales orders of the alpha- and gamma-subdivision of Proteobacteria were found at the three sites. Species and genera of the Rhodospirillales, Sphingobacteriales, Clostridiales, Oscillatoriales and Caldilineales were found only in the HIGH soil, Sphingomonadales, Burkholderiales and Pseudomonadales in the MEDIUM soil, Myxococcales in the LOW soil, and Actinomycetales in the MEDIUM and LOW soils. It was found that the largest diversity at the order and species level was found in the MEDIUM soil as bacteria of both the HIGH and LOW soils were found in it.

Respiratory and dissimilatory nitrate-reducing communities from an extreme saline alkaline soil of the former lake Texcoco (Mexico).

The diversity of the dissimilatory and respiratory nitrate-reducing communities was studied in two soils of the former lake Texcoco (Mexico). Genes encoding the membrane-bound nitrate reductase (narG) and the periplasmic nitrate reductase (napA) were used as functional markers. To investigate bacterial communities containing napA and narG in saline alkaline soils of the former lake Texcoco, libraries of the two sites were constructed (soil T3 with pH 11 and electrolytic conductivity in saturated extract (EC(SE)) 160 dS m(-1) and soil T1 with pH 8.5 and EC(SE) 0.8 dS m(-1)). Phylogenetic analysis of napA sequences separated the clone families into two main groups: dependent or independent of NapB. Most of napA sequences from site T1 were grouped in the NapB-dependent clade, meanwhile most of the napA sequences from the extreme soil T3 were affiliated to the NapB-independent group. For both sites, partial narG sequences were associated with representatives of the Proteobacteria, Firmicutes and Actinobacteria phyla, but the proportions of the clones were different. Our results support the concept of a specific and complex nitrate-reducing community for each soil of the former lake Texcoco.

Phylogenetic analysis of the archaeal community in an alkaline-saline soil of the former lake Texcoco (Mexico).

The soil of the former lake Texcoco is an extreme environment localized in the valley of Mexico City, Mexico. It is highly saline and alkaline, where Na+, Cl(-), HCO3(-) and CO3(2-) are the predominant ions, with a pH ranging from 9.8 to 11.7 and electrolytic conductivities in saturation extracts from 22 to 150 dS m(-1). Metagenomic DNA from the archaeal community was extracted directly from soil and used as template to amplify 16S ribosomal gene by PCR. PCR products were used to construct gene libraries. The ribosomal library showed that the archaeal diversity included Natronococcus sp., Natronolimnobius sp., Natronobacterium sp., Natrinema sp., Natronomonas sp., Halovivax sp., "Halalkalicoccus jeotgali" and novel clades within the family of Halobacteriaceae. Four clones could not be classified. It was found that the archaeal diversity in an alkaline-saline soil of the former lake Texcoco, Mexico, was low, but showed yet uncharacterized and unclassified species.