Microbes of the phylum Aigarchaeota are widely distributed in geothermal environments, but their physiological and ecological roles are poorly understood Here we analyze six Aigarchaeota metagenomic bins from two circumneutral hot springs in Tengchong, China, to reveal that they are either strict or facultative anaerobes, and most are chemolithotrophs that can perform sulfide oxidation Applying comparative genomics to the Thaumarchaeota and Aigarchaeota, we find that they both originated from thermal habitats, sharing 1154 genes with their common ancestor Horizontal gene transfer played a crucial role in shaping genetic diversity of Aigarchaeota and led to functional partitioning and ecological divergence among sympatric microbes, as several key functional innovations were endowed by Bacteria, including dissimilatory sulfite reduction and possibly carbon monoxide oxidation Our study expands our knowledge of the possible ecological roles of the Aigarchaeota and clarifies their evolutionary relationship to their sister lineage Thaumarchaeota

/pdf/genomic-inference-of-the-metabolism-and-evolution-of-the-1zzg2xveuc.pdf

Genomic Inference of the Metabolism and Evolution of the Archaeal Phylum Aigarchaeota

Although land use drives soil bacterial diversity and community structure, little information about the bacterial interaction networks is available. Here, we investigated bacterial co-occurrence networks in soils under different types of land use (forests, grasslands, crops and vineyards) by sampling 1798 sites in the French Soil Quality Monitoring Network covering all of France. An increase in bacterial richness was observed from forests to vineyards, whereas network complexity respectively decreased from 16,430 links to 2,046. However, the ratio of positive to negative links within the bacterial networks ranged from 2.9 in forests to 5.5 in vineyards. Networks structure was centered on the most connected genera (called hub), which belonged to Bacteroidetes in forest and grassland soils, but to Actinobacteria in vineyard soils. Overall, our study revealed that soil perturbation due to intensive cropping reduces strongly the complexity of bacterial network although the richness is increased. Moreover, the hub genera within the bacterial community shifted from copiotrophic taxa in forest soils to more oligotrophic taxa in agricultural soils.

/pdf/biogeography-of-soil-bacterial-networks-along-a-gradient-of-l4cs4637dg.pdf

Biogeography of Soil Bacterial Networks along a Gradient of Cropping Intensity.

Rhodococcus erythropolis N9T-4 shows extremely oligotrophic growth requiring atmospheric CO2 and forms its colonies on an inorganic basal medium (BM) without any additional carbon source. Screening of a random mutation library constructed by a unique genome deletion method that we established indicated that the aceA, aceB, and pckG genes encoding isocitrate lyase, malate synthase, and phosphoenolpyruvate carboxykinase, respectively, were requisite for survival on BM plates. The aceA- and aceB deletion mutants and the pckG deletion mutant grew well on BM plates containing L-malate and D-glucose, respectively, suggesting that the glyoxylate (GO) shunt and gluconeogenesis are essential for the oligotrophic growth of N9T-4. Interestingly, most of the enzyme activities in the TCA cycle were observed in the cell-free extract of N9T-4, with perhaps the most important exception being α-ketoglutarate dehydrogenase (KGDH) activity. Instead of the KGDH activity, we detected a remarkable level of α-ketoglutarate decarboxylase (KGD) activity, which is the activity exhibited by the E1 component of the KGDH complex in Mycobacterium tuberculosis. The recombinant KGD of N9T-4 catalyzed the decarboxylation of α-ketoglutarate to form succinic semialdehyde (SSA) in a time-dependent manner. Since N9T-4 also showed a detectable SSA dehydrogenase activity, we concluded that N9T-4 possesses a variant TCA cycle, which uses SSA rather than succinyl-CoA. These results suggest that oligotrophic N9T-4 cells utilize the GO shunt to avoid the loss of carbons as CO2 and to conserve CoA units in the TCA cycle.

The glyoxylate shunt is essential for CO2-requiring oligotrophic growth of Rhodococcus erythropolis N9T-4

The phylum Aquificae comprises chemolithoautotrophic thermophilic to hyperthermophilic bacteria, in which the nitrogenase reductase gene (nifH) has been reported. However, nitrogen-fixing activity has not yet been demonstrated in members of this deeply branching bacterial phylum. We isolated two thermophilic diazotrophic strains from chemosynthetic microbial communities in slightly alkaline hot springs (≥70°C) in Nakabusa, Nagano Prefecture, Japan. A phylogenetic analysis based on 16S rRNA genes identified these strains as members of the genus Hydrogenobacter within Aquificae. Their NifH sequences showed 96.5 and 97.4% amino acid sequence identities to that from Hydrogenobacter thermophilus TK-6. Nitrogenase activity, measured by acetylene reduction, was confirmed in both strains at 70°C. These novel strains grew under semi-aerobic conditions by using CO2 as the sole carbon source and N2 as the sole nitrogen source in media containing hydrogen and/or thiosulfate. To the best of our knowledge, this is the first demonstration of active nitrogen fixation in thermophilic bacteria at 70°C and in the phylum Aquificae.

Nitrogenase Activity in Thermophilic Chemolithoautotrophic Bacteria in the Phylum Aquificae Isolated under Nitrogen-Fixing Conditions from Nakabusa Hot Springs.

Previous molecular surveys indicated Acidimicrobium sp. were abundant in samples from hot (52˚C), acidic (pH 2), oligotrophic Boiling Springs Lake (BSL) in Lassen Volcanic National Park. We isolated and characterized Acidimicrobium sp. and functionally related bacteria from BSL. The pH and temperature optima of all isolates correlate with the average summer conditions of BSL suggesting these organisms are capable of active growth in BSL. Acidimicrobium isolates were capable of oxidizing iron when grown mixotrophically or autotrophically. The isolates also oxidized iron after growth cessation, suggesting a possible role of iron oxidation in maintaining homeostasis in the absence of population growth.

/pdf/isolation-and-characterization-of-novel-iron-oxidizing-4f53l5cufq.pdf

Isolation and Characterization of Novel Iron-Oxidizing Autotrophic and Mixotrophic Bacteria from Boiling Springs Lake, an Oligotrophic, Acidic Geothermal Habitat

Boiling Springs Lake (BSL) in Lassen Volcanic National Park, California, is North America's largest hot spring, but little is known about the physical, chemical, and biological features of the system. Using a remotely operated vessel, we characterized the bathymetry and near-surface temperatures at sub-meter resolution. The majority of the 1.2 ha, pH 2.2 lake is 10 m deep and 50-52 °C, but temperatures reach 93 °C locally. We extracted DNA from water and sediments collected from warm (52 °C) and hot (73-83 °C) sites separated by 180 m. Gene clone libraries and functional gene microarray (GeoChip 3.0) were used to investigate the BSL community, and uptake of radiolabeled carbon sources was used to assess the relative importance of heterotrophic vs. autotrophic production. Microbial assemblages are similar in both sites despite the strong temperature differential, supporting observations of a dynamic, convectively mixed system. Bacteria in the Actinobacteria and Aquificales phyla are abundant in the water column, and Archaea distantly related to known taxa are abundant in sediments. The functional potential appears similar across a 5-year time span, indicating a stable community with little inter-annual variation, despite the documented seasonal temperature cycle. BSL water-derived DNA contains genes for complete C, N, and S cycles, and low hybridization to probes for N and S oxidation suggests that reductive processes dominate. Many of the detected genes for these processes were from uncultivated bacteria, suggesting novel organisms are responsible for key ecosystem services. Selection imposed by low nutrients, low pH, and high temperature appear to result in low diversity and evenness of genes for key functions involved in C, N, and S cycling. Conversely, organic degradation genes appear to be functionally redundant, and the rapid assimilation of radiolabeled organic carbon into BSL cells suggests the importance of allochthonous C fueling heterotrophic production in the BSL C cycle.

/pdf/microbial-biogeochemistry-of-boiling-springs-lake-a-1iksfxkxuo.pdf

Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic, oligotrophic, low‐pH geothermal ecosystem

Preservation Potential of Lipid-Containing Viruses Under Silicifying Conditions

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Microbial biogeochemistry of Boiling Springs Lake: a physically dynamic, oligotrophic, low‐pH geothermal ecosystem

Preservation Potential of Lipid-Containing Viruses Under Silicifying Conditions