Community structures and biodeterioration processes of epilithic biofilms imply the significance of micro-environments.

Epilithic biofilms colonising outdoor stone monuments can intensify the deterioration processes of the stone materials and pose great challenges to their protection. In this study, biodiversity and community structures of the epilithic biofilms colonising the surfaces of five outdoor stone dog sculptures were characterised by high-throughput sequencing. Although they are exposed to the same envrionment in a small yard, the analysis of their biofilm populations revealed high biodiversity and species richness as well as great differences in community compostions. Interestingly, populations responsible for pigment production (e.g., Pseudomonas, Deinococcus, Sphingomonas and Leptolyngbya) and for nitrogen (e.g., Pseudomonas, Bacillus, and Beijerinckia) and sulfur cycling (e.g., Acidiphilium) were the core common taxa in the epilithic biofilms, suggesting the potential biodeterioration processes. Furthermore, significant positive corrolections of metal elements rich in stone with biofilm communities showed that epilithic biofilms could take in minerals of stone. Importantly, geochemical properties of soluble ions (higher concentration of SO42- than NO3-) and slightly acidic micro-environments on the surfaces suggest corrosion of biogenic sulfuric acids as a main mechanism of biodeterioration of the sculptures. Interestingly, relative abundacne of Acidiphilium showed a positive correlation with acidic micro-environments and SO42- concentrations, implying they could be an indicator of sulfuric acid corrosion. Together, our findings support that micro-environments are inportant to community assembly of epilithic biofilms and the biodeterioration processes involved.

Delineation of the complex microbial nitrogen-transformation network in an anammox-driven full-scale wastewater treatment plant.

Microbial-driven nitrogen removal is a crucial step in modern full-scale wastewater treatment plants (WWTPs), and the complexity of nitrogen transformation is integral to the various wastewater treatment processes. A full understanding of the overall nitrogen cycling networks in WWTPs is therefore a prerequisite for the further enhancement and optimization of wastewater treatment processes. In this study, metagenomics and metatranscriptomics were used to elucidate the microbial nitrogen removal processes in an ammonium-enriched full-scale WWTP, which was configured as an anaerobic-anoxic-anaerobic-oxic system for efficient nitrogen removal (99.63%) on a duck breeding farm. A typical simultaneous nitrification-anammox-denitrification (SNAD) process was established in each tank of this WWTP. Ammonia was oxidized by ammonia-oxidizing bacteria (AOB), archaea (AOA), and nitrite-oxidizing bacteria (NOB), and the produced nitrite and nitrate were further reduced to dinitrogen gas (N2) by anammox and denitrifying bacteria. Visible red anammox biofilms were formed successfully on the sponge carriers submerged in the anoxic tank, and the nitrogen removal rate by anammox reaction was 4.85 times higher than that by denitrification based on 15N isotope labeling and analysis. This supports the significant accumulation of anammox bacteria on the carriers responsible for efficient nitrogen removal. Two distinct anammox bacteria, named "Ca. Brocadia sp. PF01" and "Ca. Jettenia sp. PF02", were identified from the biofilm in this investigation. By recovering their genomic features and their metabolic capabilities, our results indicate that the highly active core anammox process found in PF01, suggests extending its niche within the plant. With the possible contribution of the dissimilatory nitrate reduction to ammonium (DNRA) reaction, enriching PF02 within the biofilm may also be warranted. Collectively, this study highlights the effective design strategies of a full-scale WWTP with enrichment of anammox bacteria on the carrier materials for nitrogen removal and therefore the biochemical reaction mechanisms of the contributing members.

Biofilms on stone monuments: biodeterioration or bioprotection?

Debate on whether biofilms on stone monuments are biodeteriorative or bioprotective is long-standing. We propose a criterion of 'relative bioprotective ratio' for assessing the ambivalent role of the biofilms by comparing biodeterioration with weathering. A boundary between biodeterioration and bioprotection exists and fluctuates with dynamic microflora influenced by environmental conditions.

Innovative approaches for the processes involved in microbial biodeterioration of cultural heritage materials.

Microbial colonization and development into biofilms on cultural heritage have significant implications for the deterioration of materials, particularly in the tropic and humid environments. To advance the fundamental knowledge on the biofilm-mediated (bio)deterioration processes, future investigations must focus more on the metabolically active microorganisms and biochemical reactions by a combination of methods available. Newly accessible culture-independent techniques of high-throughput sequencing and multi-omics can be coupled with culture-dependent ones and specific biochemical assays, including stable isotopes and DNA probing. Here, we describe the recent advances on this subject matter, highlight a systematic analytical approach for an integrative diagnosis of 'microbial diseases' of cultural heritage, and provide future prospects for a new paradigm of research on microbial biodeterioration of heritage materials.

[A polycyclic aromatic hydrocarbon degrading strain and its potential of degrading phenanthrene in various enhanced systems].

Polycyclic aromatic hydrocarbons (PAHs) are a class of common environmental pollutants that pose threats to human health. In this study, a mesophilic bacterial strain CFP312 (grown at 15-37 °C, optimal at 30 °C) was isolated from PAHs-contaminated soil samples. It was identified as Moraxella sp. by morphological observation, physiological and biochemical test, and 16S rRNA gene phylogeny analysis. This is the first reported PAHs degrading strains in Moraxella. Degradation analysis showed that 84% and 90% of the loaded phenanthrene (400 mg/L) were degraded within 48 h and 60 h, and the degradation rates reached 1.21 and 1.29 mg/(L·h), respectively. During the degradation of phenanthrene, phenanthrene-3,4-dihydrodiol was detected as an intermediate. Based on this, it was proposed that double oxygenation at the positions 3 and 4 of phenanthrene was the first step of biodegradation. Adaptability of strain CFP312 to different enhanced phenanthrene-degradation systems was tested in aqueous-organic system, micellar aqueous system, and cloud point system. Strain CFP312 showed good adaptability to different systems. In addition, the bacterium can rapidly degrade the phenanthrene in contaminated soil in slurry-aqueous system, indicating great potential in environmental remediation.

Synergistic interactions of Desulfovibrio and Petrimonas for sulfate-reduction coupling polycyclic aromatic hydrocarbon degradation.

Microbial sulfate-reduction coupling polycyclic aromatic hydrocarbon (PAH) degradation is an important process for the remediation of contaminated sediments. However, little is known about core players and their mechanisms in this process due to the complexity of PAH degradation and the large number of microorganisms involved. Here we analyzed potential core players in a black-odorous sediment using gradient-dilution culturing, isolation and genomic/metagenomic approaches. Along the dilution gradient, microbial PAH degradation and sulfate consumption were not decreased, and even a significant (p = 0.003) increase was observed in the degradation of phenanthrene although the microbial diversity declined. Two species, affiliated with Desulfovibrio and Petrimonas, were commonly present in all of the gradients as keystone taxa and showed as the dominant microorganisms in the single colony (SB8) isolated from the highest dilution culture with 93.49% and 4.73% of the microbial community, respectively. Desulfovibrio sp. SB8 and Petrimonas sp. SB8 could serve together as core players for sulfate-reduction coupling PAH degradation, in which Desulfovibrio sp. SB8 could degrade PAHs to hexahydro-2-naphthoyl through the carboxylation pathway while Petrimonas sp. SB8 might degrade intermediate metabolites of PAHs. This study provides new insights into the microbial sulfate-reduction coupling PAH degradation in black-odorous sediments.

Brevibacterium rongguiense sp. nov., isolated from freshwater sediment.

A Gram stain-positive, non-spore-forming, non-motile and rod-shaped actinomycete, strain 5221T, was isolated from the sediment of a river collected at Ronggui in the Pearl River Delta, PR China. Phylogenetic analysis based on 16S rRNA gene sequences revealed that the strain formed a distinct lineage within the genus Brevibacterium and had the highest sequence similarity to Brevibacterium pityocampae Tp12T (96.7 %), followed by Brevibacterium daeguense 2C6-41T (96.5 %), Brevibacterium samyangense SST-8T (96.0 %) and Brevibacterium ravenspurgense 20T (95.9 %). The results of chemotaxonomic analyses, including detecting anteiso-C15 : 0, anteiso-C17 : 0, and C16 : 0 as the major cellular fatty acids, diphosphatidylglycerol, phosphatidylglycerol and three phosphoglycolipids as the polar lipids, MK-8(H2) as the major menaquinone, and a DNA G+C content of 72.4 mol%, supported that strain 5221T is a member of the genus Brevibacterium. Furthermore, low sequence similarities of 16S rRNA gene sequences, differences in fatty acid compositions and differential physiological characteristics such as enzyme activity and carbon sources utilization ability distinguished the isolate from its close relatives. Therefore, strain 5221T represents a novel species of the genus Brevibacterium, for which the name Brevibacterium rongguiense sp. nov. is proposed, with the type strain 5221T (=GDMCC 1.1766T=KACC 21700T).

Ciceribacter ferrooxidans sp. nov., a nitrate-reducing Fe(II)-oxidizing bacterium isolated from ferrous ion-rich sediment.

A nitrate-reducing Fe(II)-oxidizing bacterial strain, F8825T, was isolated from the Fe(II)-rich sediment of an urban creek in Pearl River Delta, China. The strain was Gram-negative, facultative chemolithotrophic, facultative anaerobic, non-spore-forming, and rod-shaped with a single flagellum. Phy-logenetic analysis based on 16S rRNA gene sequencing indicated that it belongs to the genus Ciceribacter and is most closely related to C. lividus MSSRFBL1T (99.4%), followed by C. thiooxidans F43bT (98.8%) and C. azotifigens A.slu09T (98.0%). Fatty acid, polar lipid, respiratory quinone, and DNA G + C content analyses supported its classification in the genus Ciceribacter. Multilocus sequence analysis of concatenated 16S rRNA, atpD, glnII, gyrB, recA, and thrC suggested that the isolate was a novel species. DNA-DNA hybridization and genome sequence comparisons (90.88 and 89.86%, for values of ANIm and ANIb between strains F8825T with MSSRFBL1T, respectively) confirmed that strain F8825T was a novel species, different from C. lividus MSSRFBL1T, C. thiooxidans F43bT, and C. azotifigens A.slu09T. The physiological and biochemical properties of the strain, such as carbon source utilization, nitrate reduction, and ferrous ion oxidation, further supported that this is a novel species. Based on the polyphasic taxonomic results, strain F8825T was identified as a novel species in the genus Ciceribacter, for which the name Ciceribacter ferrooxidans sp. nov. is proposed. The type strain is F8825T (= CCTCC AB 2018196T = KCTC 62948T).