Occallatibacter riparius gen. nov., sp. nov. and Occallatibacter savannae sp. nov., acidobacteria isolated from Namibian soils, and emended description of the family Acidobacteriaceae

Characterization of dry-cured ham microbiota at 12 months of seasoning obtained from different rearing strategies using 16S rRNA profiling

In this study, we investigated the microbiota of 72 Italian ham samples collected after 12 months of seasoning. The hams were elaborated from pigs fed different rearing methods, including the traditional restricted medium protein diet chosen as control (C group); restrictive low protein diet (LP group); two ad libitum high-protein diet groups (HP9M group: slaughter at 9 months of age; HP170 group: slaughter at 170 kg). A multi-amplicon 16S metabarcoding approach was used, and a total of 2845 Amplicon Sequence Variants were obtained from the 72 ham samples. Main phyla included: Firmicutes (90.8%), Actinobacteria (6.2%), Proteobacteria (2.7%), and Bacteroidota (0.12%). The most common genera were Staphylococcus, Tetragenococcus, and Brevibacterium. Shannon index for α-diversity was found statistically significant, notably for the HP9M group, indicating higher diversity compared to C. PERMANOVA test on β-diversity showed significant differences in rearing methods between HP170 and C, HP170 and LP, and HP9M vs. C. All three rearing methods revealed associations with characteristic communities: the HP9M group had the highest number of associations, many of which were due to spoilage bacteria, whereas the LP group had the highest number of seasoning-favourable genera.

Edaphobacter paludis sp. nov., a new acidophilic representative of the Acidobacteriota isolated from fen soils

Two new strains JP48T and JP55 affiliated with the acidobacterial class Terriglobia have been isolated from fen soil sampled in the Fichtelgebirge Mountains near Bayreuth, Germany. Both strains were Gram-stain-negative, non-motile, non-spore-forming rods that divide by binary fission, segregate exopolysaccharide-like material and form capsules. Strains JP48T and JP55 grew at 4-36 °C (optimum at 27 °C), pH 3.6-7.3 (optimum at pH 4.6-5.5) and with NaCl concentrations of 0-3% (optimum at 1.0%; w/v). Strains JP48T and JP55 grew aerobically on a wide range of organic substrates including mono- and oligosaccharides, amino acids and short-chained fatty acids. MK-8 was identified as the major respiratory quinone. The major fatty acids for strains JP48T and JP55 were iso-C15 : 0, C16 : 1 ω7c, C16 : 0 and iso-diabolic acid. Phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, lysophophatidylethanolamine, phosphatidylcholine, unidentified glyco- and glycophospholipids, and unidentified high mass lipid species were the major polar membrane lipids. The G+C content of strains JP48T and JP55 was 57.4 and 57.2 mol%, respectively. The genomes of strains JP48T and JP55 contained nine potential secondary metabolite regions encoding for the compound classes NRPS(-like), T3PKS, terpene, or lanthipeptide class IV. Phylogenetic reconstruction and 16S rRNA gene sequence similarities of 98.3 and 96.9% identified Edaphobacter dinghuensis DHF9T and Edaphobacter lichenicola DSM 104462T as the most closely related type strains to strains JP48T and JP55. Based on their phenotype, phylogeny and chemotaxonomy, we propose the novel species Edaphobacter paludis sp. nov. (type strain JP48T=DSM 109919T=CECT 30269T; additional strain JP55=DSM 109920=CECT 30268) within the class Terriglobia of the phylum Acidobacteriota.

Amendments affect the community assembly and co-occurrence network of microorganisms in Cd and Pb tailings of the Eucalyptus camaldulensis rhizosphere

Mining tailings containing large amounts of Pb and Cd cause severe regional ecosystem pollution. Soil microorganisms play a regulatory role in the restoration of degraded ecosystems. The remediation of heavy metal-contaminated tailings with amendments and economically valuable Eucalyptus camaldulensis is a research hotspot due to its cost-effectiveness and sustainability. However, the succession and co-occurrence patterns of these microbial communities in this context remain unclear. Tailing samples of five kinds of Cd and Pb were collected in E. camaldulensis restoration models. Physicochemical properties, the proportions of different Cd and Pb forms, microbial community structure, and the co-occurrence network of rhizosphere tailings during different restoration process (organic bacterial manure, organic manure, inorganic fertilizer, bacterial agent) were considered. Organic and organic bacterial manures significantly increased pH, cation exchange capacity, and the proportion of residual Pb. Still, there was a significant decrease in the proportion of reducible Pb. The changes in microbial communities were related to physicochemical properties and the types of amendments. Organic and organic bacterium manures decreased the relative abundance of oligotrophic groups and increased the relative abundance of syntrophic groups. Inorganic fertilizers and bacterial agents decreased the relative abundance of saprophytic fungi. B. subtilis would play a better role in the environment improved by organic manure, increasing the relative abundance of beneficial microorganism and reducing the relative abundance of pathogenic microorganism. pH, cation exchange capacity, and the proportion of different forms of Pb were the main factors affecting the bacterial and fungi variation. All four amendments transformed the main critical groups of the microbial network structure from acidophilus and pathogenic microorganisms to beneficial microorganisms. Heavy metal-resistant microorganisms, stress-resistant microorganisms, beneficial microorganisms that promote nutrient cycling, and copiotrophic groups have become critical to building stable rhizosphere microbial communities. The topological properties and stability of the rhizosphere co-occurrence network were also enhanced. Adding organic and organic bacterium manures combined with E. camaldulensis to repair Cd and Pb tailings improved (1) pH and cation exchange capacity, (2) reduced the biological toxicity of Pb, (3) enhanced the stability of microbial networks, and (4) improved ecological network relationships. These positive changes are conducive to the restoration of the ecological functions of tailings.

Microbial Communities in Standing Dead Trees in Ghost Forests are Largely Aerobic, Saprophytic, and Methanotrophic

Standing dead trees (snags) are recognized for their influence on methane (CH4) cycling in coastal wetlands, yet the biogeochemical processes that control the magnitude and direction of fluxes across the snag-atmosphere interface are not fully elucidated. Herein, we analyzed microbial communities and fluxes at one height from ten snags in a ghost forest wetland. Snag-atmosphere CH4 fluxes were highly variable (- 0.11-0.51 mg CH4 m-2 h-1). CH4 production was measured in three out of ten snags; whereas, CH4 consumption was measured in two out of ten snags. Potential CH4 production and oxidation in one core from each snag was assayed in vitro. A single core produced CH4 under anoxic and oxic conditions, at measured rates of 0.7 and 0.6 ng CH4 g-1 h-1, respectively. Four cores oxidized CH4 under oxic conditions, with an average rate of - 1.13 ± 0.31 ng CH4 g-1 h-1. Illumina sequencing of the V3/V4 region of the 16S rRNA gene sequence revealed diverse microbial communities and indicated oxidative decomposition of deadwood. Methanogens were present in 20% of the snags, with a mean relative abundance of < 0.0001%. Methanotrophs were identified in all snags, with a mean relative abundance of 2% and represented the sole CH4-cycling communities in 80% of the snags. These data indicate potential for microbial attenuation of CH4 emissions across the snag-atmosphere interface in ghost forests. A better understanding of the environmental drivers of snag-associated microbial communities is necessary to forecast the response of CH4 cycling in coastal ghost forest wetlands to a shifting coastal landscape.

The effects of mixed-species root zones on the resistance of soil bacteria and fungi to long-term experimental and natural reductions in soil moisture

Mixed forest stands tend to be more resistant to drought than species-specific stands partially due to complementarity in root ecology and physiology. We asked whether complementary differences in the drought resistance of soil microbiomes might contribute to this phenomenon. We experimented on the effects of reduced soil moisture on bacterial and fungal community composition in species-specific (single species) and mixed-species root zones of Norway spruce and European beech forests in a 5-year-old throughfall-exclusion experiment and across seasonal (spring-summer-fall) and latitudinal moisture gradients. Bacteria were most responsive to changes in soil moisture, especially members of Rhizobiales, while fungi were largely unaffected, including ectomycorrhizal fungi (EMF). Community resistance was higher in spruce relative to beech root zones, corresponding with the proportions of drought-favored (more in spruce) and drought-sensitive bacterial taxa (more in beech). The spruce soil microbiome also exhibited greater resistance to seasonal changes between spring (wettest) and fall (driest). Mixed-species root zones contained a hybrid of beech- and spruce-associated microbiomes. Several bacterial populations exhibited either enhanced resistance or greater susceptibility to drought in mixed root zones. Overall, patterns in the relative abundances of soil bacteria closely tracked moisture in seasonal and latitudinal precipitation gradients and were more predictive of soil water content than other environmental variables. We conclude that complementary differences in the drought resistance of soil microbiomes can occur and the likeliest form of complementarity in mixed-root zones coincides with the enrichment of drought-tolerant bacteria associated with spruce and the sustenance of EMF by beech.

Changes in Soil Microbial Community and Carbon Flux Regime across a Subtropical Montane Peatland-to-Forest Successional Series in Taiwan

Subtropical montane peatland is among several rare ecosystems that continue to receive insufficient scientific exploration. We analyzed the vegetation types and soil bacterial composition, as well as surface carbon dioxide and methane fluxes along a successional peatland-to-upland-forest series in one such ecosystem in Taiwan. The Yuanyang Lake (YYL) study site is characterized by low temperature, high precipitation, prevailing fog, and acidic soil, which are typical conditions for the surrounding dominant Chamaecyparis obtusa var. formosana forest. Bacterial communities were dominated by Acidobacteriota and Proteobacteria. Along the bog-to-forest gradient, Proteobacteria decreased and Acidobacteriota increased while CO2 fluxes increased and CH4 fluxes decreased. Principal coordinate analysis allowed separating samples into four clusters, which correspond to samples from the bog, marsh, forest, and forest outside of the watershed. The majority of bacterial genera were found in all plots, suggesting that these communities can easily switch to other types. Variation among samples from the same vegetation type suggests influence of habitat heterogeneity on bacterial community composition. Variations of soil water content and season caused the variations of carbon fluxes. While CO2 flux decreased exponentially with increasing soil water content, the CH4 fluxes exhibited an exponential increase together with soil water content. Because YYL is in a process of gradual terrestrialization, especially under the warming climate, we expect changes in microbial composition and the greenhouse gas budget at the landscape scale within the next decades.

Paracidobacterium acidisoli gen. nov., sp. nov. and Alloacidobacterium dinghuense gen. nov., sp. nov., two acidobacteria isolated from forest soil, and reclassification of Acidobacterium ailaaui and Acidipila dinghuensis as Pseudacidobacterium ailaaui gen. nov., comb. nov. and Silvibacterium dinghuense comb. nov

Two aerobic and obligately acidophilic bacteria, designated 4G-K13T and 4Y35T, were isolated from the forest soil sampled at Dinghushan Biosphere Reserve, Guangdong Province, PR China. These two strains were Gram-stain-negative, non-motile and short rods that multiplied by binary division. Strains 4G-K13T and 4Y35T had the highest 16S rRNA gene sequence similarity of 97.0 and 97.2 % to Silvibacterium bohemicum DSM 103733T and Acidisarcina polymorpha SBC82T, respectively. Phylogenetic trees based on the 16S rRNA gene and whole genome sequences showed consistently that these two strains formed a major clade with members of the genera Acidipila , Acidisarcina , Silvibacterium and Acidobacterium in the family Acidobacteriaceae , but each occupied an unique position. In both the UBCG and the PhyloPhlAn phylogenomic trees, strains 4G-K13T and 4Y35T congruently formed a highly supported subclade with Acidobacterium capsulatum DSM 11244T and Acidobacterium ailaaui DSM 27394T, respectively. The major fatty acids (>5 %) of strain 4G-K13T were iso-C15 : 0, iso-C17 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 0 10-methyl), while that of strain 4Y35T were C16 : 0, C18 : 1  ω9c, iso-C15 : 0, summed feature 3 (C16 : 1  ω7c and/or C16 : 1  ω6c) and summed feature 9 (iso-C17 : 1  ω9c and/or C16 : 0 10-methyl). Strain 4G-K13T contained phosphatidylethanolamine, four unidentified phospholipids, four glycolipids, two unidentified aminolipids and two unknown lipids, while strain 4Y35T had phosphatidylethanolamine, three unidentified phospholipids, two glycolipids, five unidentified aminolipids and one unknown polar lipid. The DNA G+C contents of 4G-K13T and 4Y35T were 60.5 and 55.8 mol%, respectively. Based on all these phylogenetic, physiological and chemotaxonomic data, we suggest that strains 4G-K13T and 4Y35T represent two novel species of two novel genera in the family Acidobacteriaceae , for which the names Paracidobacterium acidisoli gen. nov., sp. nov. (type strain: 4G-K13T=GDMCC 1.1195T=NBRC 113249T) and Alloacidobacterium dinghuense gen. nov., sp. nov. (type strain: 4Y35T=KACC 21728T=NBRC 114261T) are proposed. We also propose to reclassify Acidobacterium ailaaui and Acidipila dinghuensis as Pseudacidobacterium ailaaui gen. nov., comb. nov. and Silvibacterium dinghuense comb. nov., respectively, based mainly on the results of phylogenomic analysis.

Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén

Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.

Differential Response of Acidobacteria to Water Content, Soil Type, and Land Use During an Extended Drought in African Savannah Soils

Although climate change is expected to increase the extent of drylands worldwide, the effect of drought on the soil microbiome is still insufficiently understood as for dominant but little characterized phyla like the Acidobacteria. In the present study the active acidobacterial communities of Namibian soils differing in type, physicochemical parameters, and land use were characterized by high-throughput sequencing. Water content, pH, major ions and nutrients were distinct for sandy soils, woodlands or dry agriculture on loamy sands. Soils were repeatedly sampled over a 2-year time period and covered consecutively a strong rainy, a dry, a normal rainy and a weak rainy season. The increasing drought had differential effects on different soils. Linear modeling of the soil water content across all sampling locations and sampling dates revealed that the accumulated precipitation of the preceding season had only a weak, but statistically significant effect, whereas woodland and irrigation exerted a strong positive effect on water content. The decrease in soil water content was accompanied by a pronounced decrease in the fraction of active Acidobacteria (7.9-0.7%) while overall bacterial community size/cell counts remained constant. Notably, the strongest decline in the relative fraction of Acidobacteria was observed after the first cycle of rainy and dry season, rather than after the weakest rainy season at the end of the observation period. Over the 2-year period, also the β-diversity of soil Acidobacteria changed. During the first year this change in composition was related to soil type (loamy sand) and land use (woodland) as explanatory variables. A total of 188 different acidobacterial sequence variants affiliated with the "Acidobacteriia," Blastocatellia, and Vicinamibacteria changed significantly in abundance, suggesting either drought sensitivity or formation of dormant cell forms. Comparative physiological testing of 15 Namibian isolates revealed species-specific and differential responses in viability during long-term continuous desiccation or drying-rewetting cycles. These different responses were not determined by phylogenetic affiliation and provide a first explanation for the effect of drought on soil Acidobacteria. In conclusion, the response of acidobacterial communities to water availability is non-linear, most likely caused by the different physiological adaptations of the different taxa present.

Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils

The presence of genes for glycosyl hydrolases in many Acidobacteria genomes indicates an important role in the degradation of plant cell wall material. Acidobacteria bacterium AB60 was obtained from Cerrado oligotrophic soil in Brazil, where this phylum is abundant. The 16S rRNA gene analyses showed that AB60 was closely related to the genera Occallatibacter and Telmatobacter. However, AB60 grew on xylan as carbon source, which was not observed in Occallatibacter species; but growth was not detected on medium containing carboxymethyl cellulose, as observed in Telmatobacter. Nevertheless, the genome analysis of AB60 revealed genes for the enzymes involved in cellulose as well as xylan degradation. In addition to enzymes involved in xylan degradation, α-l-rhamnosidase was detected in the cultures of AB60. Functional screening of a small-insert genomic library did not identify any clones capable of carboxymethyl cellulose degradation, but open reading frames coding α-l-arabinofuranosidase and α-l-rhamnosidase were present in clones showing xylan degradation halos. Both enzymes act on the lateral chains of heteropolymers such as pectin and some hemicelluloses. These results indicate that the hydrolysis of α-linked sugars may offer a metabolic niche for slow-growing Acidobacteria, allowing them to co-exist with other plant-degrading microbes that hydrolyze β-linked sugars from cellulose or hemicellulose backbones.

High Diversity and Functional Potential of Undescribed "Acidobacteriota" in Danish Wastewater Treatment Plants

Microbial communities in water resource recovery facilities encompass a large diversity of poorly characterized lineages that could have undescribed process-critical functions. Recently, it was shown that taxa belonging to "Acidobacteriota" are abundant in Danish full-scale activated sludge wastewater treatment plants (WWTP), and here we investigated their diversity, distribution, and functional potential. "Acidobacteriota" taxa were identified using a comprehensive full-length 16S rRNA gene reference dataset and amplicon sequencing surveys across 37 WWTPs. Members of this phylum were diverse, belonging to 14 families, eight of which are completely uncharacterized and lack type strains. Several lineages were abundant, with relative abundances of up to 5% of the microbial community. Genome annotation and metabolic reconstruction of 50 high-quality "Acidobacteriota" metagenome-assembled genomes (MAGs) from 19 WWTPs showed high metabolic diversity and potential involvement in nitrogen and phosphorus removal and iron reduction. Fluorescence in situ hybridization (FISH) using newly-designed probes revealed cells with diverse morphologies, predominantly located inside activated sludge flocs. FISH in combination with Raman microspectroscopy revealed ecophysiological traits in probe-defined cells from the families Holophagaceae, Thermoanaerobaculaceae, and Vicinamibacteraceae, and families with the placeholder name of midas_f_502, midas_f_973, and midas_f_1548. Members of these lineages had the potential to be polyphosphate-accumulating organisms (PAOs) as intracellular storage was observed for the key compounds polyphosphate and glycogen.

Priming Effects of Cover Cropping on Bacterial Community in a Tea Plantation

The acidic nature of red soil commonly found in tea plantations provides unique niches for bacterial growth. These bacteria as well as soil properties are dynamic and vary with agricultural management practices. However, less is known about the influence of manipulation such as cover cropping on bacterial communities in tea plantations. In this study a field trial was conducted to address the short-term effects of soybean intercropping on a bacterial community. Diversity, metabolic potential and structure of the bacterial community were determined through community level physiological profiling and amplicon sequencing approaches. Cover cropping was observed to increase soil EC, available P, K, and microelements Fe, Mn, Cu, and Zn after three months of cultivation. Bacterial functional diversity and metabolic potential toward six carbon source categories also increased in response to cover cropping. Distinct bacterial communities among treatments were revealed, and the most effective biomarkers, such as Acidobacteriaceae, Burkholderiaceae, Rhodanobacteraceae, and Sphingomonadaceae, were identified in cover cropping. Members belonging to these families are considered as organic matter decomposers and/or plant growth promoting bacteria. We provided the first evidence that cover cropping boosted both copiotrophs (Proteobacteria) and oligotrophs (Acidobacteria), with potentially increased functional stability, facilitated nutrient cycling, and prospective benefits to plants in the tea plantation.

Distribution patterns of Acidobacteriota in different fynbos soils

The Acidobacteriota is ubiquitous and is considered as one of the major bacterial phyla in soils. The current taxonomic classifications of this phylum are divided into 15 class-level subdivisions (SDs), with only 5 of these SDs containing cultured and fully described species. Within the fynbos biome, the Acidobacteriota has been reported as one of the dominant bacterial phyla, with relative abundances ranging between 4–26%. However, none of these studies reported on the specific distribution and diversity of the Acidobacteriota within these soils. Therefore, in this study we aimed to first determine the relative abundance and diversity of the Acidobacteriota in three pristine fynbos nature reserve soils, and secondly, whether differences in the acidobacterial composition can be attributed to environmental factors, such as soil abiotic properties. A total of 27 soil samples were collected at three nature reserves, namely Jonkershoek, Hottentots Holland, and Kogelberg. The variable V4-V5 region of the 16S rRNA gene was sequenced using the Ion Torrent S5 platform. The mean relative abundance of the Acidobacteriota were 9.02% for Jonkershoek, 14.91% for Kogelberg, and most significantly (p<0.05), 18.42% for Hottentots Holland. A total of 33 acidobacterial operational taxonomic units (OTUs) were identified. The dominant subdivisions identified in all samples included SDs 1, 2, and 3. Significant differences were observed in the distribution and composition of these OTUs between nature reserves. The SD1 were negatively correlated to soil pH, hydrogen (H⁺), potassium (K⁺) and carbon (C). In contrast, SD2, was positively correlated to soil pH, phosphorus (P), and K⁺, and unclassified members of SD3 was positively correlated to H⁺, K, and C. This study is the first to report on the specific acidobacterial distribution in pristine fynbos soils in South Africa.

Soil Acidobacteria Strain AB23 Resistance to Oxidative Stress Through Production of Carotenoids

Metagenomic studies revealed the prevalence of Acidobacteria in soils, but the physiological and ecological reasons for their success are not well understood. Many Acidobacteria exhibit carotenoid-related pigments, which may be involved in their tolerance of environmental stress. The aim of this work was to investigate the role of the orange pigments produced by Acidobacteria strain AB23 isolated from a savannah-like soil and to identify putative carotenoid genes in Acidobacteria genomes. Phylogenetic analysis revealed that strain AB23 belongs to the Occallatibacter genus from the class Acidobacteriia (subdivision 1). Strain AB23 produced carotenoids in the presence of light and vitamins; however, the growth rate and biomass decreased when cells were exposed to light. The presence of carotenoids resulted in tolerance to hydrogen peroxide. Comparative genomics revealed that all members of Acidobacteriia with available genomes possess the complete gene cluster for phytoene production. Some Acidobacteriia members have an additional gene cluster that may be involved in the production of colored carotenoids. Both colored and colorless carotenoids are involved in tolerance to oxidative stress. These results show that the presence of carotenoid genes is widespread among Acidobacteriia. Light and atmospheric oxygen stimulate carotenoid synthesis, but there are other natural sources of oxidative stress in soils. Tolerance to environmental oxidative stress provided by carotenoids may offer a competitive advantage for Acidobacteria in soils.

Soil Bacterial and Archaeal Communities and Their Potential to Perform N-Cycling Processes in Soils of Boreal Forests Growing on Well-Drained Peat

Peatlands are unique wetland ecosystems that cover approximately 3% of the world’s land area and are mostly located in boreal and temperate regions. Around 15 Mha of these peatlands have been drained for forestry during the last century. This study investigated soil archaeal and bacterial community structure and abundance, as well as the abundance of marker genes of nitrogen transformation processes (nitrogen fixation, nitrification, denitrification, and dissimilatory nitrate reduction to ammonia) across distance gradients from drainage ditches in nine full-drained, middle-aged peatland forests dominated by Scots pine, Norway spruce, or Downy birch. The dominating tree species had a strong effect on the chemical properties (pH, N and C/N status) of initially similar Histosols and affected the bacterial and archaeal community structure and abundance of microbial groups involved in the soil nitrogen cycle. The pine forests were distinguished by having the lowest fine root biomass of trees, pH, and N content and the highest potential for N fixation. The distance from drainage ditches affected the spatial distribution of bacterial and archaeal communities (especially N-fixers, nitrifiers, and denitrifiers possessing nosZ clade II), but this effect was often dependent on the conditions created by the dominance of certain tree species. The composition of the nitrifying microbial community was dependent on the soil pH, and comammox bacteria contributed significantly to nitrate formation in the birch and spruce soils where the pH was higher than 4.6. The highest N₂O emission was recorded from soils with higher bacterial and archaeal phylogenetic diversity such as birch forest soils. This study demonstrates that the long-term growth of forests dominated by birch, pine, and spruce on initially similar organic soil has resulted in tree-species-specific changes in the soil properties and the development of forest-type-specific soil prokaryotic communities with characteristic functional properties and relationships within microbial communities.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria)

Palaeontologically, eubacteria are > 3× older than neomura (eukaryotes, archaebacteria). Cell biology contrasts ancestral eubacterial murein peptidoglycan walls and derived neomuran N-linked glycoprotein coats/walls. Misinterpreting long stems connecting clade neomura to eubacteria on ribosomal sequence trees (plus misinterpreted protein paralogue trees) obscured this historical pattern. Universal multiprotein ribosomal protein (RP) trees, more accurate than rRNA trees, are taxonomically undersampled. To reduce contradictions with genically richer eukaryote trees and improve eubacterial phylogeny, we constructed site-heterogeneous and maximum-likelihood universal three-domain, two-domain, and single-domain trees for 143 eukaryotes (branching now congruent with 187-protein trees), 60 archaebacteria, and 151 taxonomically representative eubacteria, using 51 and 26 RPs. Site-heterogeneous trees greatly improve eubacterial phylogeny and higher classification, e.g. showing gracilicute monophyly, that many 'rDNA-phyla' belong in Proteobacteria, and reveal robust new phyla Synthermota and Aquithermota. Monoderm Posibacteria and Mollicutes (two separate wall losses) are both polyphyletic: multiple outer membrane losses in Endobacteria occurred separately from Actinobacteria; neither phylum is related to Chloroflexi, the most divergent prokaryotes, which originated photosynthesis (new model proposed). RP trees support an eozoan root for eukaryotes and are consistent with archaebacteria being their sisters and rooted between Filarchaeota (=Proteoarchaeota, including 'Asgardia') and Euryarchaeota sensu-lato (including ultrasimplified 'DPANN' whose long branches often distort trees). Two-domain trees group eukaryotes within Planctobacteria, and archaebacteria with Planctobacteria/Sphingobacteria. Integrated molecular/palaeontological evidence favours negibacterial ancestors for neomura and all life. Unique presence of key pre-neomuran characters favours Planctobacteria only as ancestral to neomura, which apparently arose by coevolutionary repercussions (explained here in detail, including RP replacement) of simultaneous outer membrane and murein loss. Planctobacterial C-1 methanotrophic enzymes are likely ancestral to archaebacterial methanogenesis and β-propeller-α-solenoid proteins to eukaryotic vesicle coats, nuclear-pore-complexes, and intraciliary transport. Planctobacterial chaperone-independent 4/5-protofilament microtubules and MamK actin-ancestors prepared for eukaryote intracellular motility, mitosis, cytokinesis, and phagocytosis. We refute numerous wrong ideas about the universal tree.

Rhizobacterial community structure in response to nitrogen addition varied between two Mollisols differing in soil organic carbon

Excessive nitrogen (N) fertilizer input to agroecosystem fundamentally alters soil microbial properties and subsequent their ecofunctions such as carbon (C) sequestration and nutrient cycling in soil. However, between soils, the rhizobacterial community diversity and structure in response to N addition is not well understood, which is important to make proper N fertilization strategies to alleviate the negative impact of N addition on soil organic C and soil quality and maintain plant health in soils. Thus, a rhizo-box experiment was conducted with soybean grown in two soils, i.e. soil organic C (SOC)-poor and SOC-rich soil, supplied with three N rates in a range from 0 to 100 mg N kg⁻¹. The rhizospheric soil was collected 50 days after sowing and MiSeq sequencing was deployed to analyze the rhizobacterial community structure. The results showed that increasing N addition significantly decreased the number of phylotype of rhizobacteria by 12.3%, and decreased Shannon index from 5.98 to 5.36 irrespective of soils. Compared to the SOC-rich soil, the increases in abundances of Aquincola affiliated to Proteobacteria, and Streptomyces affiliated to Actinobacteria were greater in the SOC-poor soil in response to N addition. An opposite trend was observed for Ramlibacter belong to Proteobacteria. These results suggest that N addition reduced the rhizobacterial diversity and its influence on rhizobacterial community structure was soil-specific.

Pheno- and Genotyping of Hopanoid Production in Acidobacteria

Hopanoids are pentacyclic triterpenoid lipids synthesized by different bacterial groups. Methylated hopanoids were believed to be exclusively synthesized by cyanobacteria and aerobic methanotrophs until the genes encoding for the methylation at the C-2 and C-3 position (hpnP and hpnR) were found to be widespread in the bacterial domain, invalidating their use as specific biomarkers. These genes have been detected in the genome of the Acidobacterium "Ca. Koribacter versatilis," but our knowledge of the synthesis of hopanoids and the presence of genes of their biosynthetic pathway in other member of the Acidobacteria is limited. We analyzed 38 different strains of seven Acidobacteria subdivisions (SDs 1, 3, 4, 6, 8, 10, and 23) for the presence of C30 hopenes and C30+ bacteriohopane polyols (BHPs) using the Rohmer reaction. BHPs and/or C30 hopenes were detected in all strains of SD1 and SD3 but not in SD4 (excepting Chloracidobacterium thermophilum), 6, 8, 10, and 23. This is in good agreement with the presence of genes required for hopanoid biosynthesis in the 31 available whole genomes of cultivated Acidobacteria. All genomes encode the enzymes involved in the non-mevalonate pathway ultimately leading to farnesyl diphosphate but only SD1 and 3 Acidobacteria and C. thermophilum encode all three enzymes required for the synthesis of squalene, its cyclization (shc), and addition and modification of the extended side chain (hpnG, hpnH, hpnI, hpnJ, hpnO). In almost all strains, only tetrafunctionalized BHPs were detected; three strains contained variable relative abundances (up to 45%) of pentafunctionalized BHPs. Only "Ca. K. versatilis" contained methylated hopanoids (i.e., 2,3-dimethyl bishomohopanol), although in low (<10%) amounts. These genes are not present in any other Acidobacterium, consistent with the absence of methylated BHPs in the other examined strains. These data are in agreement with the scattered occurrence of methylated BHPs in other bacterial phyla such as the Alpha-, Beta-, and Gammaproteobacteria and the Cyanobacteria, limiting their biomarker potential. Metagenomes of Acidobacteria were also examined for the presence of genes required for hopanoid biosynthesis. The complete pathway for BHP biosynthesis was evident in SD2 Acidobacteria and a group phylogenetically related to SD1 and SD3, in line with the limited occurrence of BHPs in acidobacterial cultures.

Luteitalea pratensis gen. nov., sp. nov. a new member of subdivision 6 Acidobacteria isolated from temperate grassland soil

Albeit being widespread and abundant in soils worldwide, bacteria of the phylum Acidobacteria have remained grossly understudied due to difficulties in their cultivation and isolation. To date, only 48 species have been validly described, including a single member of the phylogenetically diverse Acidobacteria subdivision 6. Here, we report the polyphasic characterization of strain HEG_-6_39T, a novel representative of Acidobacteria subdivision 6 isolated from a grassland soil in Thuringia, Germany. Cells of HEG_-6_39T are Gram-stain-negative, non-motile, non-spore-forming, non-capsulated short rods that form small dark yellow colonies. This slow growing bacterium is psychrotolerant and grows between 0 and 36 °C. It displays a narrower pH tolerance (5.3-8.3) than most acidobacteria. The strain is an aerobe that grows chemo-organotrophically utilizing mostly sugars and proteinaceous substrates such as peptone, yeast extract, casein hydrolysate and casamino acids as substrates. Diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol and two unknown phospholipids are identified as polar lipids. Major fatty acids are iso-C15 : 0, summed feature 3 (C16 : 1ω6c/C16 : 1ω7c), C18 : 1ω9c and iso-C17 : 1ω9c. The major respiratory quinone is MK-8. The G+C content of the genomic DNA is 64.7 mol%. 16S rRNA gene sequence analysis indicated that this bacterium was related to Vicinamibacter silvestris Ac_5_C6T with 93.6 % sequence similarity. Based on the present taxonomic characterization, strain HEG_-6_39T represents a new species of a novel genus for which the name Luteitalea pratensis gen. nov., sp. nov., is proposed. The type strain of the type species is HEG_-6_39T (=DSM 100886T=KCTC 52215T).

Population densities of indigenous Acidobacteria change in the presence of plant growth promoting rhizobacteria (PGPR) in rhizosphere

Rhizosphere microbial community has diverse metabolic capabilities and plays a crucial role in maintaining plant health. Oligotrophic plant growth promoting rhizobacteria (PGPR), along with difficult-to-culture microbial fractions, might be involved synergistically in microbe-microbe and plant-microbe interactions in the rhizosphere. Among the difficult-to-culture microbial fractions, Acidobacteria constitutes the most dominant phylum thriving in rhizospheric soils. We selected effective PGPR for tomato and black gram and studied their effect on population densities of acidobacterial members. Three facultatively oligotrophic PGPR were identified through 16S rRNA gene sequencing as Sphingobacterium sp. (P3), Variovorax sp. (P4), and Roseomonas sp. (A2); the latter being a new report of PGPR. In presence of selected PGPR strains, the changes in population densities of Acidobacteria were monitored in metagenomic DNA extracted from bulk and rhizospheric soils of tomato and black gram using real time qPCR. A gradual increase in equivalent cell numbers of Acidobacteria members was observed over time along with a simultaneous increase in plant growth promotion by test PGPR. We report characterization of three effective PGPR strains and their effects on indigenous, underexplored difficult-to-culture phylum-Acidobacteria. We suggest that putative interactions between these two bacterial groups thriving in rhizospheric soils could be beneficial for plant growth.

Defining the taxonomic status of described subdivision 3 Acidobacteria: proposal of Bryobacteraceae fam. nov

The phylum Acidobacteria represents one of the highly diverse but poorly characterized phylogenetic groups of the domain Bacteria. The taxonomically described acidobacteria belong to 27 genera and 49 species, which represent subdivisions 1, 3, 4, 6, 8, 10 and 23 of this phylum. However, the corresponding family ranks have been defined only for some of these characterized micro-organisms. Here, we suggest the establishment of a novel family, Bryobacteraceae fam. nov., to accommodate taxonomically described members of subdivision 3 Acidobacteria. This family is characterized by Gram-stain-negative, non-spore-forming and non-motile rods, which divide by binary fission. Members of this family are mildly acidophilic, mesophilic, aerobic and facultatively anaerobic chemoheterotrophs that utilize various sugars and polysaccharides. The major fatty acids are iso-C15 : 0 and C16 : 1ω7c; the cells also contain significant amounts of 13,16-dimethyloctacosanedioic (iso-diabolic) acid. Currently, the family comprises the genera Bryobacter and Paludibaculum.

Acidicapsa ferrireducens sp. nov., Acidicapsa acidiphila sp. nov., and Granulicella acidiphila sp. nov.: novel acidobacteria isolated from metal-rich acidic waters

Four novel strains of Acidobacteria were isolated from water samples taken from pit lakes at two abandoned metal mines in the Iberian Pyrite Belt mining district, south-west Spain. Three of the isolates belong to the genus Acidicapsa (MCF9^T, MCF10^T, and MCF14) and one of them to the genus Granulicella (MCF40^T). All isolates are moderately acidophilic (pH growth optimum 3.8-4.1) and mesophilic (temperature growth optima 30-32 °C). Isolates MCF10^T and MCF40^T grew at pH lower (<3.0) than previously reported for all other acidobacteria. All four strains are obligate heterotrophs and metabolised a wide range of sugars. While all four isolates are obligate aerobes, MCF9^T, MCF10^T, and MCF14 catalysed the reductive dissolution of the ferric iron mineral schwertmannite when incubated under micro-aerobic conditions. Isolates MCF9^T and MCF14 shared 99.5% similarity of their 16 S rRNA genes, and were considered to be strains of the same species. The major quinone of strains MCF10^T, MCF9^T, and MCF40^T is MK-8, and their DNA G + C contents are 60.0, 59.7, and 62.1 mol%, respectively. Based on phylogenetic and phenotypic data, three novel species, Acidicapsa ferrireducens strain MCF9^T (=DSM 28997^T = NCCB 100575^T), Acidicapsa acidiphila strain MCF10^T (=DSM 29819^T = NCCB 100576^T), and Granulicella acidiphila strain MCF40^T (DSM 28996^T = NCCB 100577^T), are proposed.

Brevitalea aridisoli, B. deliciosa and Arenimicrobium luteum, three novel species of Acidobacteria subdivision 4 (class Blastocatellia) isolated from savanna soil and description of the novel family Pyrinomonadaceae

Three novel strains of the phylum Acidobacteria (Ac_11_E3T, Ac_12_G8T and Ac_16_C4T) were isolated from Namibian semiarid savanna soils by a high-throughput cultivation approach using low-nutrient growth media. 16S rRNA gene sequence analysis placed all three strains in the order Blastocatellales of the class Blastocatellia (Acidobacteria subdivision 4). However, 16S rRNA gene sequence similarities to their closest relative Pyrinomonas methylaliphatogenes K22T were ≤90 %. Cells of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were Gram-staining-negative and non-motile and divided by binary fission. Ac_11_E3T and Ac_16_C4T formed white colonies, while those of Ac_12_G8T were orange-yellowish. All three strains were aerobic chemoorganoheterotrophic mesophiles with a broad pH range for growth. All strains used a very limited spectrum of carbon and energy sources for growth, with a preference for complex proteinaceous substrates. The major respiratory quinone was MK-8. The major shared fatty acid was iso-C15 : 0. The DNA G+C contents of strains Ac_11_E3T, Ac_12_G8T and Ac_16_C4T were 55.9 mol%, 66.9 mol% and 54.7 mol%, respectively. Based on these characteristics, the two novel genera Brevitaleagen. nov. and Arenimicrobiumgen. nov. are proposed, harboring the novel species Brevitaleaaridisoli sp. nov. (Ac_11_E3T=DSM 27934T=LMG 28618T), Brevitalea deliciosa sp. nov. (Ac_16_C4T=DSM 29892T=LMG 28995T) and Arenimicrobium luteum sp. nov. (Ac_12_G8T=DSM 26556T=LMG 29166T), respectively. Since these novel genera are only distantly related to established families, we propose the novel family Pyrinomonadaceaefam. nov. that accommodates the proposed genera and the genus Pyrinomonas(Crowe et al., 2014).

The Ecology of Acidobacteria: Moving beyond Genes and Genomes

The phylum Acidobacteria is one of the most widespread and abundant on the planet, yet remarkably our knowledge of the role of these diverse organisms in the functioning of terrestrial ecosystems remains surprisingly rudimentary. This blatant knowledge gap stems to a large degree from the difficulties associated with the cultivation of these bacteria by classical means. Given the phylogenetic breadth of the Acidobacteria, which is similar to the metabolically diverse Proteobacteria, it is clear that detailed and functional descriptions of acidobacterial assemblages are necessary. Fortunately, recent advances are providing a glimpse into the ecology of members of the phylum Acidobacteria. These include novel cultivation and enrichment strategies, genomic characterization and analyses of metagenomic DNA from environmental samples. Here, we couple the data from these complementary approaches for a better understanding of their role in the environment, thereby providing some initial insights into the ecology of this important phylum. All cultured acidobacterial type species are heterotrophic, and members of subdivisions 1, 3, and 4 appear to be more versatile in carbohydrate utilization. Genomic and metagenomic data predict a number of ecologically relevant capabilities for some acidobacteria, including the ability to: use of nitrite as N source, respond to soil macro-, micro nutrients and soil acidity, express multiple active transporters, degrade gellan gum and produce exopolysaccharide (EPS). Although these predicted properties allude to a competitive life style in soil, only very few of these prediction shave been confirmed via physiological studies. The increased availability of genomic and physiological information, coupled to distribution data in field surveys and experiments, should direct future progress in unraveling the ecology of this important but still enigmatic phylum.