Rubellimicrobium thermophilum gen. nov., sp. nov., a red-pigmented, moderately thermophilic bacterium isolated from coloured slime deposits in paper machines

Fog caused distinct diversity of airborne bacterial communities enriched with pathogens over central Indo-Gangetic plain in India

Fog causes enhancement of bacterial loading in the atmosphere. Current study represents the impact of occurrences of fog on the alteration of diversity of airborne bacteria and their network computed from metagenomic data of airborne samples collected at Arthauli (25.95°N, 85.10°E) situated at central Indo-Gangetic Plain (IGP) during 1-14 January 2021. A distinct bacterial diversity with a complex network is identified in foggy condition due to the enrichment of unique types of bacteria. Present investigation highlights a statistically significant enrichment of airborne pathogenic bacteria found in a unique ecosystem within air evolved due to the occurrences of fog over central IGP. In the foggy network, Cutibacterium, an opportunistic pathogen, is identified to be interacting maximum (21 edges) with other bacteria with statistically significant copresence relation, which are responsible for various infections for human beings. A 40-60% increase (p < 0.01) in the abundance of pathogenic bacteria for respiratory and skin diseases is noticed in fog period. Among the fog-enriched bacteria, Cutibacterium, Herbaspirillum, Paenibacillus, and Tsukamurella are examples of opportunistic bacteria causing various respiratory diseases, while Paenibacillus can even cause skin cancer and acute lymphoblastic leukemia.

Rubellimicrobium arenae sp. nov., isolated from desert soil

Two Gram-stain-negative strains, designated as SYSU D00286^T and SYSU D00782, were isolated from a sand sample collected from the Kumtag Desert in Xinjiang, north-west China. Cells were aerobic, non-motile and positive for both oxidase and catalase. Growth occurred at 4-37 °C (optimum, 28-30 °C), pH 6.0-7.0 (optimum, pH 7.0) and NaCl concentration of 0-1.5 % (w/v; optimum, 0%). Growth was observed on Reasoner's 2A agar and nutrient agar, but not on Luria-Bertani agar and trypticase soy agar. The polar lipids were identified as diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, three unidentified aminolipids, one unidentified glycolipid and two unidentified phospholipids. The major respiratory quinone was ubiquinone-10 and the major fatty acids (>10 %) were C_16 : 0 and summed feature 8 (C_18 : 1  ω7c and/or C_18 : 1  ω6c). The 16S rRNA gene sequence similarity between strains SYSU D00286^T and SYSU D00782 was 100%, and their average nucleotide identity (ANI), average amino acid identity and (AAI) digital DNA-DNA hybridization (dDDH) values were all 100.0 %. Phylogenetic analysis indicated that these two strains belong to the same species of the genus Rubellimicrobium and show the highest sequence similarity to Rubellimicrobium rubrum KCTC 72461^T (98.2 %) and Rubellimicrobium roseum CCTCC AA 208029^T (97.5 %). The ANI, AAI and dDDH values between SYSU D00286^T (as well as SYSU D00782) and the other five Rubellimicrobium type strains were all less than or equal to 83.2, 80.1 and 23.6 %, respectively. Based on their phylogenetic, phenotypic and chemotaxonomical features, strains SYSU D00286^T and SYSU D00782 represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium arenae sp. nov. is proposed. The type strain is SYSU D00286^T (=MCCC 1K04981^T=CGMCC 1.8626^T=KCTC 82271^T).

Use of Metagenomic Whole Genome Shotgun Sequencing Data in Taxonomic Assignment of Dipterygium glaucum Rhizosphere and Surrounding Bulk Soil Microbiomes, and Their Response to Watering

The metagenomic whole genome shotgun sequencing (mWGS) approach was used to detect signatures of the rhizosphere microbiomes of Dipterygium glaucum and surrounding bulk soil microbiomes, and to detect differential microbial responses due to watering. Preliminary results reflect the reliability of the experiment and the rationality of grouping microbiomes. Based on the abundance of non-redundant genes, bacterial genomes showed the highest level, followed by Archaeal and Eukaryotic genomes, then, the least abundant viruses. Overall results indicate that most members of bacteria have a higher abundance/relative abundance (AB/RA) pattern in the rhizosphere towards plant growth promotion, while members of eukaryota have a higher pattern in bulk soil, most likely acting as pathogens. The results also indicate the contribution of mycorrhiza (genus Rhizophagus) in mediating complex mutualistic associations between soil microbes (either beneficial or harmful) and plant roots. Some of these symbiotic relationships involve microbes of different domains responding differentially to plant root exudates. Among these are included the bacterial genus Burkholderia and eukaryotic genus Trichoderma, which have antagonistic activities against the eukaryotic genus Fusarium. Another example involves Ochrobactrum phage POA1180, its bacterial host and plant roots. One of the major challenges in plant nutrition involves other microbes that manipulate nitrogen levels in the soil. Among these are the microbes that perform contraversal actions of nitrogen fixation (the methanogen Euryarchaeota) and ammonia oxidation (Crenarchaeota). The net nitrogen level in the soil is originally based on the AB/RA of these microbes and partially on the environmental condition. Watering seems to influence the AB/RA of a large number of soil microbes, where drought-sensitive microbes (members of phyla Acidobacteria and Gemmatimonadetes) showed an increased AB/RA pattern after watering, while others (Burkholderia and Trichoderma) seem to be among microbes assisting plants to withstand abiotic stresses. This study sheds light on the efficient use of mWGS in the taxonomic assignment of soil microbes and in their response to watering. It also provides new avenues for improving biotic and abiotic resistance in domestic plant germplasm via the manipulation of soil microbes.

Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape

In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbor a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems. This article is protected by copyright. All rights reserved.

A novel organic carbon accumulation mechanism in croplands in the Yellow River Delta, China

The trends and mechanisms of organic carbon changes in coastal delta croplands are not yet clear due to the complexity physicochemical processes in soil. In this study, combing powder x-ray diffraction (XRD), microbial analysis, and density functional theory in quantum mechanics, we proposed a novel mechanism underlying OC accumulation. We investigated changes of three kinds of organic carbon (OC)-dissolved organic carbon (DOC), light fraction organic carbon (LFOC), and heavy fraction organic carbon (HFOC) in the Yellow River Delta croplands. We found that HFOC, dominant in coastal delta cropland soil, formed at different ages and its density increased with increasing reclamation time. Yet, DOC and LFOC had no significant increase or decrease tendency. Moreover, in coastal delta croplands, HFOC accumulation might be a complex progress, including the loss of indigenous OC and the accumulation of newly input OC. Based on these results, we proposed that although root exudative DOC (organic acids) could cause the indigenous OC loss by forming a specific microbial community, it still was a source of HFOC and promoted the OC accumulation. More importantly, based on density functional theory, we verified that these root exudative organic acids could adsorb on SiO₂ together with crystalline Fe oxides (Fe_c) to form aggregates. The finding could explain the phenomenon that the XRD results showed samples were compounds of SiO₂, Fe_c, and OC and the accumulation of HFOC in coastal delta croplands. By revealing a new OC accumulation mechanism in coastal delta croplands, this study provides novel insights into the mechanism of OC dynamics in coastal delta croplands and the global carbon budget.

Phospholipid N-methyltransferases produce various methylated phosphatidylethanolamine derivatives in thermophilic bacteria

One of the most common pathways for the biosynthesis of the phospholipid phosphatidylcholine (PC) in bacteria is the successive three-fold N-methylation of phosphatidylethanolamine (PE) catalyzed by phospholipid N-methyltransferases (Pmts). Pmts with different activities have been described in a number of mesophilic bacteria. In the present study, we identified and characterized the substrate and product spectrum of four Pmts from thermophilic bacteria. Three of these enzymes were purified in an active form. The Pmts from Melghirimyces thermohalophilus, Thermochromogena staphylospora and Thermobifida fusca produce monomethyl-PE (MMPE) and dimethyl-PE (DMPE). T. fusca encodes two Pmt candidates, one is mutationally inactivated and the other is responsible for the accumulation of large amounts of MMPE. The Pmt enzyme from Rubellimicrobium thermophilum catalyzes all three methylation reactions to synthesize PC. Moreover, we show that PE, previously reported to be absent in R. thermophilum, is in fact produced and serves as precursor for the methylation pathway. In an alternative route, the strain is able to produce PC by the PC synthase pathway when choline is available. The activity of all purified thermophilic Pmt enzymes was stimulated by anionic lipids suggesting membrane recruitment of these cytoplasmic proteins via electrostatic interactions. Our study provides novel insights into the functional characteristics of phospholipid N-methyltransferases in a previously unexplored set of thermophilic environmental bacteria. Importance In recent years, the presence of phosphatidylcholine (PC) in bacterial membranes has gained increasing attention, partly due to its critical role in the interaction with eukaryotic hosts. PC biosynthesis via a three-step methylation of phosphatidylethanolamine, catalyzed by phospholipid N-methyltransferases (Pmts), has been described in a range of mesophilic bacteria. Here, we expand our knowledge on bacterial PC formation by the identification, purification and characterization of Pmts from phylogenetically diverse thermophilic bacteria, and thereby provide insights into the functional characteristics of Pmt enzymes in thermophilic actinomycetes and proteobacteria.

A Novel Moderately Thermophilic Facultative Methylotroph within the Class Alphaproteobacteria

Methylotrophic bacteria (non-methanotrophic methanol oxidizers) consuming reduced carbon compounds containing no carbon–carbon bonds as their sole carbon and energy source have been found in a great variety of environments. Here, we report a unique moderately thermophilic methanol-oxidising bacterium (strain LS7-MT) that grows optimally at 55 °C (with a growth range spanning 30 to 60 °C). The pure isolate was recovered from a methane-utilizing mixed culture enrichment from an alkaline thermal spring in the Ethiopia Rift Valley, and utilized methanol, methylamine, glucose and a variety of multi-carbon compounds. Phylogenetic analysis of the 16S rRNA gene sequences demonstrated that strain LS7-MT represented a new facultatively methylotrophic bacterium within the order Hyphomicrobiales of the class Alphaproteobacteria. This new strain showed 94 to 96% 16S rRNA gene identity to the two methylotroph genera, Methyloceanibacter and Methyloligella. Analysis of the draft genome of strain LS7-MT revealed genes for methanol dehydrogenase, essential for methanol oxidation. Functional and comparative genomics of this new isolate revealed genomic and physiological divergence from extant methylotrophs. Strain LS7-MT contained a complete mxaF gene cluster and xoxF1 encoding the lanthanide-dependent methanol dehydrogenase (XoxF). This is the first report of methanol oxidation at 55 °C by a moderately thermophilic bacterium within the class Alphaproteobacteria. These findings expand our knowledge of methylotrophy by the phylum Proteobacteria in thermal ecosystems and their contribution to global carbon and nitrogen cycles.

Bioremoval of graffiti using novel commercial strains of bacteria

Previous studies have provided evidence that bioremediation deals a novel approach to graffiti removal, thereby overcoming well-known limitations of current cleaning methods. In the present study eight bacteria aerobic, mesophilic and culturable from the American ATCC and the German DSMZ collections of microorganisms, some isolated from car paint waste, colored deposits in a pulp dryer and wastewater from dye works, were tested in the removal of silver and black graffiti spray paints using immersion strategies with glass slides. Absorbance at 600 nm and live/dead assays were performed to estimate bacterial density and activity in all samples. Also, pH and dissolved organic carbon (DOC) and inorganic carbon (DIC) measurements in the liquid media were made, as well as, thickness, colorimetric and infrared (FTIR) spectroscopy measurements in graffiti paint layers were used to evaluate the presence of the selected bacteria in the samples and the graffiti bioremoval capacity of bacteria. Data demonstrated that of the eight bacteria studied, Enterobacter aerogenes, Comamonas sp. and a mixture of Bacillus sp., Delftia lacustris, Sphingobacterium caeni, and Ochrobactrum anthropi were the most promising for bioremoval of graffiti. According to significant changes in FTIR spectra, indicating an alteration of the paint polymeric structure, coupled with the presence of a consistent quantity of live bacteria in the medium as well as a significant increase of DIC (a measure of metabolic activity) and a change in paint color.

Falling bacterial communities from the atmosphere

BACKGROUND

Bacteria emitted into the atmosphere eventually settle to the pedosphere via sedimentation (dry deposition) or precipitation (wet deposition), constituting a part of the global cycling of substances on Earth, including the water cycle. In this study, we aim to investigate the taxonomic compositions and flux densities of bacterial deposition, for which little is known regarding the relative contributions of each mode of atmospheric deposition, the taxonomic structures and memberships, and the aerodynamic properties in the atmosphere.

RESULTS

Precipitation was found to dominate atmospheric bacterial deposition, contributing to 95% of the total flux density at our sampling site in Korea, while bacterial communities in precipitation were significantly different from those in sedimentation, in terms of both their structures and memberships. Large aerodynamic diameters of atmospheric bacteria were observed, with an annual mean of 8.84 μm, which appears to be related to their large sedimentation velocities, with an annual mean of 1.72 cm s^- 1 for all bacterial taxa combined. The observed mean sedimentation velocity for atmospheric bacteria was larger than the previously reported mean sedimentation velocities for fungi and plants.

CONCLUSIONS

Large aerodynamic diameters of atmospheric bacteria, which are likely due to the aggregation and/or attachment to other larger particles, are thought to contribute to large sedimentation velocities, high efficiencies as cloud nuclei, and large amounts of precipitation of atmospheric bacteria. Moreover, the different microbiotas between precipitation and sedimentation might indicate specific bacterial involvement and/or selective bacterial growth in clouds. Overall, our findings add novel insight into how bacteria participate in atmospheric processes and material circulations, including hydrological circulation, on Earth.

Effects of co-loading of polyethylene microplastics and ciprofloxacin on the antibiotic degradation efficiency and microbial community structure in soil

Microplastics (MPs) have become a global environmental concern while soil plastic pollution has been largely overlooked. In view of the severe antibiotic contamination in arable soils owing to land application of sewage sludge and animal manure, the invasion of MPs along with antibiotics may pose an unpredictable threat to soil microbial communities and ecological health. In this work, polyethylene MPs and ciprofloxacin (CIP) were applied to a soil microcosm to investigate the CIP degradation behavior and their combined effects on soil microbial communities. Compared with that of the individual amendment of CIP, the co-amendment of CIP and MPs reduced the CIP degradation efficiency during the 35 d cultivation period. In addition, the high-throughput sequencing results illustrated that the combined loading of MPs and CIP in soil significantly decreased the microbial diversity compared with that of individual contamination. As for the community structure, the microbial compositions at the phylum level were consistent among all treatments, and the most dominant phyla were Proteobacteria, Actinobacteria, and Chloroflexi. At the genus level, only one genus, namely Arthrobacter, was remarkably changed in the CIP-amended soil compared with that in the blank control, but four genera were significantly altered in the MPs-CIP co-amended soil. Serratia and Achromobacter were abundant in the combined polluted soil, which might have been involved in accelerated depletion of soil total nitrogen based on redundancy analysis. These findings may contribute to the understanding of bacterial responses to the combined pollution of MPs and antibiotics in soil ecosystems.

Rubellimicrobium rubrum sp. nov., a novel bright reddish bacterium isolated from a lichen sample

A novel strain, YIM 131921^T, was isolated from a Physcia sp. lichen collected from the South Bank Forest of the Baltic Sea. The strain is Gram-negative, catalase positive and oxidase negative, strictly aerobic, asporogenous, non-motile and reddish brown in colour. The temperature and pH for growth were found to be 20-30 °C (optimum 28 °C) and pH 6.5-12.0 (optimum pH 7.0 ± 0.5). No growth was observed in the presence of NaCl. Based on 16S rRNA gene sequence similarity, strain YIM 131921^T shares high similarities with Rubellimicrobium roseum YIM 48858^T (98.3%), followed by Rubellimicrobium mesophilum MSL-20^T (96.8%), Rubellimicrobium aerolatum 5715S-9^T (96.1%) and Rubellimicrobium thermophilum DSM 16684^T (96.0%). Phylogenetic trees showed YIM 131921^T forms a cluster with type strains of the genus Rubellimicrobium. The predominant cellular fatty acids (> 20%) were identified as summed feature 8 (C_18:1ω7c) and C_16:0. Q-10 was found to be the predominant respiratory ubiquinone. The polar lipids were identified as diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, glycolipid, phospholipids and an unidentified aminolipid. The DNA G + C content of the draft genome sequence is 66.6 mol%. Strain YIM 131921^T showed an average nucleotide identity value of 80.3% and a digital DNA-DNA hybridizations value of 26.1% with the reference strain R. roseum YIM 48858^T based on draft genome sequences. Based on comparative analyses of phenotypic, molecular, chemotaxonomic data and genomic comparisons, strain YIM 131921^T is concluded to represent a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium rubrum sp. nov. is proposed. The type strain is YIM 131921^T (= CGMCC 1.13958^T = NBRC 114054^T = KCTC 72461^T).

Bacterial Dormancy Is More Prevalent in Freshwater than Hypersaline Lakes

Bacteria employ a diverse array of strategies to survive under extreme environmental conditions but maintaining these adaptations comes at an energetic cost. If energy reserves drop too low, extremophiles may enter a dormant state to persist. We estimated bacterial dormancy and identified the environmental variables influencing our activity proxy in 10 hypersaline and freshwater lakes across the Western United States. Using ribosomal RNA:DNA ratios as an indicator for bacterial activity, we found that the proportion of the community exhibiting dormancy was 16% lower in hypersaline than freshwater lakes. Based on our indicator variable multiple regression results, saltier conditions in both freshwater and hypersaline lakes increased activity, suggesting that salinity was a robust environmental filter structuring bacterial activity in lake ecosystems. To a lesser degree, higher total phosphorus concentrations reduced dormancy in all lakes. Thus, even under extreme conditions, the competition for resources exerted pressure on activity. Within the compositionally distinct and less diverse hypersaline communities, abundant taxa were disproportionately active and localized in families Microbacteriaceae (Actinobacteria), Nitriliruptoraceae (Actinobacteria), and Rhodobacteraceae (Alphaproteobacteria). Our results are consistent with the view that hypersaline communities are able to capitalize on a seemingly more extreme, yet highly selective, set of conditions and finds that extremophiles may need dormancy less often to thrive and survive.

Global Association between Thermophilicity and Vancomycin Susceptibility in Bacteria

Exploration of the aquatic microbiota of several circum-neutral (6.0-8.5 pH) mid-temperature (55-85°C) springs revealed rich diversities of phylogenetic relatives of mesophilic bacteria, which surpassed the diversity of the truly-thermophilic taxa. To gain insight into the potentially-thermophilic adaptations of the phylogenetic relatives of Gram-negative mesophilic bacteria detected in culture-independent investigations we attempted pure-culture isolation by supplementing the enrichment media with 50 μg ml(-1) vancomycin. Surprisingly, this Gram-positive-specific antibiotic eliminated the entire culturable-diversity of chemoorganotrophic and sulfur-chemolithotrophic bacteria present in the tested hot water inocula. Moreover, it also killed all the Gram-negative hot-spring isolates that were obtained in vancomycin-free media. Concurrent literature search for the description of Gram-negative thermophilic bacteria revealed that at least 16 of them were reportedly vancomycin-susceptible. While these data suggested that vancomycin-susceptibility could be a global trait of thermophilic bacteria (irrespective of their taxonomy, biogeography and Gram-character), MALDI Mass Spectroscopy of the peptidoglycans of a few Gram-negative thermophilic bacteria revealed that tandem alanines were present in the fourth and fifth positions of their muropeptide precursors (MPPs). Subsequent phylogenetic analyses revealed a close affinity between the D-alanine-D-alanine ligases (Ddl) of taxonomically-diverse Gram-negative thermophiles and the thermostable Ddl protein of Thermotoga maritima, which is well-known for its high specificity for alanine over other amino acids. The Ddl tree further illustrated a divergence between the homologs of Gram-negative thermophiles and mesophiles, which broadly coincided with vancomycin-susceptibility and vancomycin-resistance respectively. It was thus hypothesized that thermophilic Ddls have been evolutionarily selected to favor a D-ala-D-ala bonding. However, preference for D-ala-D-ala-terminated MPPs does not singlehandedly guarantee vancomycin susceptibility of thermophilic bacteria as the large and relatively-hydrophilic vancomycin molecule has to cross the outer membrane before it can inhibit peptidoglycan biosynthesis. Literature shows that many mesophilic Gram-negative bacteria also have D-ala-D-ala-terminated MPPs, but they still remain resistant to vancomycin due to the relative impermeability of their membranes. But the global vancomycin-susceptibility phenotype of thermophilic bacteria itself testifies that the drug crosses the membrane in all these cases. As a corollary, it seems quite likely that the outer membranes of thermophilic bacteria have some yet-unknown characteristic feature(s) that invariably ensures the entry of vancomycin.

Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309(T)), a representative of the Roseobacter group isolated from soil, and emended description of the species

Rubellimicrobium mesophilum Dastager et al. 2008 is a mesophilic and light reddish-pigmented representative of the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae. Representatives of the Roseobacter group play an important role in the marine biogeochemical cycles and were found in a broad variety of marine environments associated with algal blooms, different kinds of sediments, and surfaces of invertebrates and vertebrates. Roseobacters were shown to be widely distributed, especially within the total bacterial community found in coastal waters, as well as in mixed water layers of the open ocean. Here we describe the features of R. mesophilum strain MSL-20^T together with its genome sequence and annotation generated from a culture of DSM 19309^T. The 4,927,676 bp genome sequence consists of one chromosome and probably one extrachromosomal element. It contains 5,082 protein-coding genes and 56 RNA genes. As previously reported, the G+C content is significantly different from the actual genome sequence-based G+C content and as the type strain tests positively for oxidase, the species description is emended accordingly. The genome was sequenced as part of the activities of the Transregional Collaborative Research Centre 51 (TRR51) funded by the German Research Foundation (DFG).

Genome sequence of the reddish-pigmented Rubellimicrobium thermophilum type strain (DSM 16684(T)), a member of the Roseobacter clade

Rubellimicrobium thermophilum Denner et al. 2006 is the type species of the genus Rubellimicrobium, a representative of the Roseobacter clade within the Rhodobacteraceae. Members of this clade were shown to be abundant especially in coastal and polar waters, but were also found in microbial mats and sediments. They are metabolically versatile and form a physiologically heterogeneous group within the Alphaproteobacteria. Strain C-Ivk-R2A-2(T) was isolated from colored deposits in a pulp dryer; however, its natural habitat is so far unknown. Here we describe the features of this organism, together with the draft genome sequence and annotation and novel aspects of its phenotype. The 3,161,245 bp long genome contains 3,243 protein-coding and 45 RNA genes.

Mini-review: microbial problems in paper production

Paper mills are open systems, which provide favorable conditions for microbial growth. Microbial contamination can cause substantial economic losses, including the deterioration of raw materials, interference with production processes by breakdowns and lowering product quality, and eventually, problems in wastewater treatment. Damage is caused by acidification, attack on raw materials, the formation of odorous products, discoloration of pigments, and the formation of methane and hydrogen, thereby producing potentially explosive conditions. Population analyses have revealed that a wide variety of microorganisms are involved, but there appear to be no typical strains associated with paper mills. Current trends in process engineering, such as chlorine-free bleaching, processing at neutral pH, closed cycles, and the use of recycled paper also favor microbial growth and biofilm (slime) formation. A fundamental problem associated with slimes is the extensive matrix of extracellular polymeric substances, which is composed of a large variety of highly hydrated polysaccharides, proteins, nucleic acids, and lipids. No 'silver bullet' against biofouling can be expected, and effective countermeasures have to be based on holistic approaches.

Bacterial indicator of agricultural management for soil under no-till crop production

The rise in the world demand for food poses a challenge to our ability to sustain soil fertility and sustainability. The increasing use of no-till agriculture, adopted in many areas of the world as an alternative to conventional farming, may contribute to reduce the erosion of soils and the increase in the soil carbon pool. However, the advantages of no-till agriculture are jeopardized when its use is linked to the expansion of crop monoculture. The aim of this study was to survey bacterial communities to find indicators of soil quality related to contrasting agriculture management in soils under no-till farming. Four sites in production agriculture, with different soil properties, situated across a west-east transect in the most productive region in the Argentinean pampas, were taken as the basis for replication. Working definitions of Good no-till Agricultural Practices (GAP) and Poor no-till Agricultural Practices (PAP) were adopted for two distinct scenarios in terms of crop rotation, fertilization, agrochemicals use and pest control. Non-cultivated soils nearby the agricultural sites were taken as additional control treatments. Tag-encoded pyrosequencing was used to deeply sample the 16S rRNA gene from bacteria residing in soils corresponding to the three treatments at the four locations. Although bacterial communities as a whole appeared to be structured chiefly by a marked biogeographic provincialism, the distribution of a few taxa was shaped as well by environmental conditions related to agricultural management practices. A statistically supported approach was used to define candidates for management-indicator organisms, subsequently validated using quantitative PCR. We suggest that the ratio between the normalized abundance of a selected group of bacteria within the GP1 group of the phylum Acidobacteria and the genus Rubellimicrobium of the Alphaproteobacteria may serve as a potential management-indicator to discriminate between sustainable vs. non-sustainable agricultural practices in the Pampa region.

Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India

A novel aerobic bacterium, strain HT23(T), able to grow on 500 mM sodium arsenate was isolated from a hot-spring sediment sample collected from Athamallik, Orissa, India. Cells of this isolate were Gram negative. Heterotrophic growth was observed at pH 6.0-11.0 and 20-45 °C. Optimum growth was observed at 37 °C and pH 7.0-10.0. The major polar lipids are diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidyl choline and phosphatidyl monomethyl ethanolamine. The major isoprenoid quinone was Q-10. 16S rRNA gene sequence analysis indicated that the bacterium clustered with the genus Pannonibacter and showed 98.9 % similarity with Pannonibacter phragmitetus C6-19(T) (DSM 14782(T)) and 98 % with the P. phragmitetus group B and P. phragmitetus group E strains. Levels of DNA-DNA relatedness between the strain HT23(T) and P. phragmitetus C6-19(T) (DSM 14782(T)) and other strains of P. phragmitetus group B and group E strains were below 55 %. On the basis of phenotypic and chemotaxonomic characteristics, 16S rRNA gene sequence analysis and DNA-DNA hybridization data, strain HT23(T) is considered to represent a novel species of the genus Pannonibacter, for which the name Pannonibacter indica sp. nov. is proposed. The type strain is HT23(T) (=JCM 16851(T) = DSM 23407(T) = LMG 25769(T)).

Breaking through a phylogenetic impasse: a pair of associated archaea might have played host in the endosymbiotic origin of eukaryotes

For over a century, the origin of eukaryotes has been a topic of intense debate among scientists. Although it has become widely accepted that organelles such as the mitochondria and chloroplasts arose via endosymbiosis, the origin of the eukaryotic nucleus remains enigmatic. Numerous models for the origin of the nucleus have been proposed over the years, many of which use endosymbiosis to explain its existence. Proposals of microbes whose ancestors may have served as either a host or a guest in various endosymbiotic scenarios abound, none of which have been able to sufficiently incorporate the cell biological as well as phylogenetic data which links these organisms to the nucleus. While it is generally agreed that eukaryotic nuclei share more features in common with archaea rather than with bacteria, different studies have identified either one or the other of the two major groups of archaea as potential ancestors, leading to somewhat of a stalemate. This paper seeks to resolve this impasse by presenting evidence that not just one, but a pair of archaea might have served as host to the bacterial ancestor of the mitochondria. This pair may have consisted of ancestors of both Ignicoccus hospitalis as well as its ectosymbiont/ectoparasite ‘Nanoarchaeum equitans’.

Rubellimicrobium roseum sp. nov., a Gram-negative bacterium isolated from the forest soil sample

A novel pink-coloured, non-spore-forming, non-motile, Gram-negative bacterium, designated YIM 48858(T), is described by using a polyphasic approach. The strain can grow at pH 6.5-9 (optimum at pH 7) and 25-30 degrees C (optimum at 28 degrees C). NaCl is not required for its growth. Positive for oxidase and catalase. Urease activity, nitrate reduction, starch and Tween 80 tests are negative reaction. 16S rRNA gene sequence similarity studies showed that strain YIM 48858(T) is a member of the genus Rubellimicrobium, with similarities of 96.3, 95.7 and 95.5% to Rubellimicrobium mesophilum MSL-20(T), Rubellimicrobium aerolatum 5715S-9(T) and Rubellimicrobium thermophilum DSM 16684(T), respectively. Q-10 was the predominant respiratory ubiquinone as in the other members of the genus Rubellimicrobium. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphoglycolipid, glycolipid and the major fatty acids were C18:1 omega7c, C16:0 and C10:0 3-OH, which are very different from the valid published species. The DNA G + C content was 67.7 mol%. Both phylogenetic and chemotaxonomic evidence supports that YIM 48858(T) is a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium roseum sp. nov. is proposed. The type strain is YIM 48858(T) (=CCTCC AA 208029(T) =KCTC 23202(T)).

Chelatococcus sambhunathii sp. nov., a moderately thermophilic alphaproteobacterium isolated from hot spring sediment

A moderately thermophilic bacterial strain (HT4T) isolated from a hot spring sediment was characterized phenotypically and phylogenetically. Cells were Gram-negative, aerobic, non-sporulating, rod-shaped and motile by means of a single polar flagellum. Both oxidase and catalase activities were positive. Heterotrophic growth was observed at pH 6.0–8.5 and at 20–50 °C; optimum growth occurred at pH 7.5–8.0 and 37–42 °C. The major cellular fatty acids were C14 : 0 3-OH, C18 : 0 3-OH, C18 : 1 2-OH, C18 : 1 ω7c and C19 : 0 cyclo ω8c. The DNA G+C content of strain HT4T was 67.8 mol%.16S rRNA gene sequence analysis indicated that strain HT4T clustered within the radiation of the genus Chelatococcus and showed 99.0 % similarity with Chelatococcus daeguensis CCUG 54519T and 96 % similarity with Chelatococcus asaccharovorans DSM 6462T. However, levels of DNA–DNA relatedness between strain HT4T and Chelatococcus daeguensis CCUG 54519T and Chelatococcus asaccharovorans DSM 6462T were 52 and 20 %, respectively. On the basis of the phenotypic, physiological and chemotaxonomic data, 16S rRNA gene sequence analysis and DNA–DNA hybridization results, strain HT4T is considered to represent a novel species of the genus Chelatococcus, for which the name Chelatococcus sambhunathii sp. nov. is proposed. The type strain is HT4T (=DSM 18167T=JCM 14988T).

Early succession of bacterial biofilms in paper machines

Formation of biofilms causes severe problems in paper machines, and hence financial costs. It would be preferable to prevent attachment of the primary-colonizing bacteria than to control the growth of secondary communities, which are sheltered by exopolysaccharide slime layers. We have therefore investigated the early succession of paper-machine biofilms by incubating stainless-steel test coupons in the process water-flow lines in two paper machines operating in slightly alkaline conditions in temperatures (45 and 49 degrees C) supporting thermophilic microbes. Microbial succession was profiled using length heterogeneity analysis of PCR-amplified 16S rRNA genes (LH-PCR) and linking the sequence data of the created 16S rRNA gene libraries to the dominant LH-PCR peaks. Although the bacterial fingerprints obtained from the attached surface communities varied slightly in different samples, the biomarker signals of the dominating primary-colonizing bacterial groups remained high over time in each paper machine. Most of the 16S rRNA gene copies in the early biofilms were assigned to the genera Rhodobacter, Tepidimonas, and Cloacibacterium. The dominance of these sequence types decreased in the developing biofilms. Finally, as phylogenetically identical primary-colonizers were detected in the two different paper mills, the machines evidently had similar environmental conditions for bacterial growth and potentially a common source of contamination.

Rubellimicrobium aerolatum sp. nov., isolated from an air sample in Korea

A pink-coloured bacterial strain, designated 5715S-9(T), was isolated from an air sample collected in Suwon, Republic of Korea. The cells were strictly aerobic, Gram-negative, non-spore-forming, non-flagellated and short-rod-shaped. On the basis of 16S rRNA gene sequence analysis, the organism was a member of the genus Rubellimicrobium, showing the highest sequence similarities with Rubellimicrobium mesophilum MSL-20(T) (96.2 % sequence similarity) and Rubellimicrobium thermophilum DSM 16684(T) (93.9 %). The major polar lipids were phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, phosphatidylethanolamine and an unidentified glycolipid. The major fatty acids (>10 %) were C(18 : 1)omega7c, C(16 : 0) and 11-methyl C(18 : 1)omega7c. The G+C content of the DNA was 69 mol%. On the basis of both phylogenetic and phenotypic evidence, strain 5715S-9(T) represents a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium aerolatum sp. nov. is proposed. The type strain is 5715S-9(T) (=KACC 12504(T)=DSM 19297(T)).

Rubellimicrobium mesophilum sp. nov., a mesophilic, pigmented bacterium isolated from soil

A pink- to light-reddish-pigmented, aerobic, pointed, budding, mesophilic strain designated MSL-20T was isolated from soil from Bigeum island, Korea. The isolate was Gram-negative. Cells were motile rods without flagella. The temperature and pH for growth were 20-37 degrees C (optimum 28 degrees C) and pH 7.0-11.0 (optimum pH 7.0+/-0.2). Q-10 was the predominant respiratory ubiquinone. The major fatty acids were C16:0 (37 %), C18: 1 omega7c (36 %) and 11-methyl C18:1 omega7c (12 %). Phylogenetic analysis based on the 16S rRNA gene sequence revealed that Rubellimicrobium thermophilum DSM 16684T was its closest neighbour (95.2 % similarity); the isolate had less than 97.0 % similarity to all species with validly published names. Chemotaxonomic data were determined for this isolate, including peptidoglycan type, diagnostic sugar composition, fatty acid profiles, ubiquinones and polar lipids; the results supported the affiliation of strain MSL-20T to the genus Rubellimicrobium. The DNA G+C content was 72.3 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic data, strain MSL-20(T) represents a novel species of the genus Rubellimicrobium, for which the name Rubellimicrobium mesophilum sp. nov. is proposed. The type strain is MSL-20T (=KCTC 22012T =DSM 19309T).

Diversity, ecology, and genomics of the Roseobacter clade: a short overview

Due to worldwide distribution, high abundance and availability of physiologically diverse isolates the Roseobacter clade is one of the most intensively studied groups of marine bacteria. Organisms of this clade have been detected in a large variety of habitats, from coastal regions to deep-sea sediments and from polar ice to tropical latitudes, and constitute up to 25% of the total bacterial community. Use of a multitude of organic compounds, sulfur oxidation, aerobic anoxygenic photosynthesis, oxidation of carbon monoxide, DMSP demethylation, and production of secondary metabolites are some of the important traits found in this clade. Physiological characteristics and the different isolation sources indicate that organisms of the Roseobacter clade occupy various ecological niches. Since the first description of Roseobacter spp. in 1991, 38 affiliated and validated genera have been described. More than half of these descriptions have been published within the last 3 years. Genome sequencing of currently 40 different strains demonstrates enormous interest in the genetic and metabolic diversity of these bacteria. Plasmids with an enormous size range are also widespread in the Roseobacter clade indicating an adaptive genomic structure. Comparisons with other highly relevant groups, like the SAR11 clade, have shown drastic differences in genome organization.

Wenxinia marina gen. nov., sp. nov., a novel member of the Roseobacter clade isolated from oilfield sediments of the South China Sea

An aerobic and heterotrophic, Gram-negative bacterial isolate, strain HY34T, was isolated from sediment of an oilfield in the South China Sea, China. The taxonomy of strain HY34T was studied by phenotypic and phylogenetic methods. Strain HY34T formed faint-pink colonies on marine agar 2216. Cells of strain HY34T were non-motile, ovoid or short rods. Strain HY34T was positive for catalase and oxidase, and nitrate was reduced to nitrite. The nearly complete 16S rRNA gene sequence of strain HY34T was obtained and sequence analysis showed that it, together with the genus Rubellimicrobium, formed a distinct clade close to some members of the Roseobacter clade in the family Rhodobacteraceae, and it showed highest sequence similarities to Oceanicola granulosus HTCC2516T (93.8 %), Silicibacter lacuscaerulensis ITI-1157T (93.3 %), Dinoroseobacter shibae DFL 12T (93.3 %) and Rubellimicrobium thermophilum C-lvk-R2A-2T (92.2 %). Bacteriochlorophyll a was not detected. The ubiquinone system was Q-10. The major polar lipids were phosphatidylglycerol, phosphatidylcholine and an unidentified glycolipid. The major fatty acids (>10 %) were C18 : 1 ω7c and C16 : 0. The DNA G+C content of this strain was 69.4 mol%. A polyphasic analysis supported the conclusion that this strain represents a novel genus and species, which we designated Wenxinia marina gen. nov., sp. nov. The type strain of Wenxinia marina is HY34T (=CGMCC 1.6105T =JCM 14017T).