Mycobacteria isolated from angkor monument sandstones grow chemolithoautotrophically by oxidizing elemental sulfur

Metagenomic study of the microbiome and key geochemical potentials associated with architectural heritage sites: a case study of the Song Dynasty city wall in Shou County, China

Historical cultural heritage sites are valuable for all of mankind, as they reflect the material and spiritual wealth of by nations, countries, or specific groups during the development of human civilization. The types and functions of microorganisms that form biofilms on the surfaces of architectural heritage sites influence measures to preserve and protect these sites. These microorganisms contribute to the biocorrosion of architectural heritage structures through the cycling of chemical elements. The ancient city wall of Shou County is a famous architectural and cultural heritage site from China's Song Dynasty, and the protection and study of this site have substantial historical and cultural significance. In this study, we used metagenomics to study the microbial diversity and taxonomic composition of the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study covered three main topics: (1) examining the distribution of bacteria in the biofilm on the surfaces of the Song Dynasty city wall in Shou County; (2) predicting the influence of bacteria involved in the C, N, and S cycles on the corrosion of the city wall via functional gene analysis; and (3) discussing cultural heritage site protection measures for biocorrosion-related bacteria to investigate the impact of biocorrosion on the Song Dynasty city wall in Shou County, a tangible example of Chinese cultural heritage. The study revealed that (1) the biofilm bacteria mainly belonged to Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes, which accounted for more than 70% of the total bacteria in the biofilms. The proportion of fungi in the microbial community of the well-preserved city wall was greater than that in the damaged city wall. The proportion of archaea was low-less than 1%. (2) According to the Shannon diversity index, the well-preserved portion of the ancient city wall had the highest diversity of bacteria, fungi, and archaea, and bacterial diversity on the good city wall was greater than that on the corroded city wall. (3) Bray-Curtis distances revealed that the genomes of the two good city walls were similar and that the genomes of the corroded city wall portions were similar. Researchers also detected human intestine-related bacteria in four locations on the city walls, with the proportion of these bacteria in the microbial community being greater on good city walls than on bad city walls. (4) KEGG functional analysis revealed that the energy metabolism and inorganic ion transport activities of the bacterial community on the corroded city wall were greater than those of the good city wall. (5) In the carbon cycle, the absence of active glycolysis, the ED pathway, and the TCA cycle played significant roles in the collapse of the east city wall. (6) The nitrogen cycling processes involved ammonia oxidation and nitrite reduction to nitrate. (7) In the sulfur cycle, researchers discovered a crucial differential functional gene, SoxY, which facilitates the conversion of thiosulfate to sulfate. This study suggests that, in the future, biological approaches can be used to help cultural heritage site protectors achieve targeted and precise protection of cultural relics through the use of microbial growth inhibition technology. The results of this study serve as a guide for the protection of cultural heritage sites in other parts of China and provide a useful supplement to research on the protection of world cultural heritage or architectural heritage sites.

Ecological strategies of bacterial communities in prehistoric stone wall paintings across weathering gradients: A case study from the Borana zone in southern Ethiopia

Rock art paintings represent fragile ecosystems supporting complex microbial communities tuned to the lithic substrate and climatic conditions. The composition and activity of these microbial communities associated with different weathering patterns affecting rock art sites remain unexplored. This study aimed to explore how bacterial communities adapt their ecological strategies based on substrate weathering, while also examining the role of their metabolic pathways in either biodeterioration or bioprotection of the underlying stone. SEM-EDS investigations coupled with 16S rRNA gene sequencing and PICRUSt2 analysis were applied on different weathered surfaces that affect southern Ethiopian rock paintings to investigate the relationships between the current stone microbiome and weathering patterns. The findings revealed that samples experiencing low and high weathering reached a climax stage characterized by stable microenvironments and limited resources. This condition favored K-strategist microorganisms, leading to reduced α-biodiversity and a community with a positive or neutral impact on the substrate. In contrast, moderately-weathered samples displayed diverse microhabitats, resulting in the prevalence of r-strategist bacteria, increased α-biodiversity, and the presence of specialist microorganisms. Moreover, the bacterial communities in moderately-weathered samples demonstrated the highest potential for carbon fixation, stress responses, and complete nitrogen and sulfur cycles. This bacterial community also showed the potential to negatively impact the underlying substrate. This research provided valuable insights into the little-understood ecology of bacterial communities inhabiting deteriorated surfaces, shedding light on the potential role of these microorganisms in the sustainable conservation of rock art.

Microscopic evidence of sandstone deterioration and damage by fungi isolated from the Angkor monuments in simulation experiments

The Angkor monuments have been registered on the World Cultural Heritage List of UNESCO, while the buildings built mostly of sandstone are suffering from serious deterioration and damage. Microorganisms are one of the leading causes for the sandstone deterioration. Identification of the mechanisms underlying the biodeterioration is of significance because it reveals the biochemical reaction involved so that effective conservation and restoration of cultural properties can be achieved. In this study, the fungal colonization and biodeterioration of sandstone in simulation experiments were examined using confocal reflection microscopy (CRM) and scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS). Aspergillus sp. strain AW1 and Paecilomyces sp. strain BY8 isolated from the deteriorated sandstone of Angkor Wat and Bayon of Angkor Thom, respectively, were inoculated and incubated with the sandstone used for construction of Angkor Wat. With CRM, we could visualize that strain AW1 tightly attached to and broke in the sandstone with extension of the hyphae. Quantitative imaging analyses showed that the sandstone surface roughness increased and the cavities formed under the fungal hyphae deepened during the incubation of strains AW1 and BY8. These highlighted that the massive growth of fungi even under the culture conditions was associated with the cavity formation of the sandstone and its expansion. Furthermore, SEM-EDS indicated the flat and Si-rich materials, presumably quartz and feldspar, were found frequently at the intact sandstone surface. But the flatness was lost during the incubation, possibly due to the detachment of the Si-rich mineral particles by the fungal deterioration. Consequently, this study proposed a biodeterioration model of the sandstone in that the hyphae of fungi elongated on the surface of the sandstone to penetrate into the soft and porous sandstone matrix, damaging the matrix and gradually destabilize the hard and Si-rich minerals, such as quartz and feldspar, to the collapse and cavities.

Bats, monkeys and plants in the time of Covid-19 pandemic at Angkor monuments

Knowledge of biodeterioration and protection of cultural heritage depends on the scientific understanding of the substratum materials, the ambient environment, the fauna and flora including the microorganisms so an overall picture can be constructed to serve as a basis for protection and management. Over the past more than 20 years of survey and research, an accumulated dataset is available on the mechanisms on the (bio)deterioration of stone monuments in Cambodia, involving interactions among water cycling and salt dynamics with the presence of a rich surface microbiome, the biofilms. However, during the Covid-19 period (2020-2022), because of a drastic drop on tourist population, the number of bats and monkeys are on the rising, which have an impact on the on-going protection efforts. At the same time, large trees around and on the cultural heritage sites are being managed by trimming and removal to decrease the potential risk and negative impacts from them. The new management scheme needs scientific results for the long-term successful protection of these cultural heritage. A close examination of these issues is also meaningful and important to the research new initiatives and policy to be implemented not only in Cambodia but also elsewhere.

Characteristics of biotrickling filter system for hydrogen sulfide removal with seasonal temperature variations: A strategy for low temperature conditions

The impact of temperature on the biological removal of hydrogen sulfide (H₂S) from air is critical to its effective application in cold regions or seasons. This study investigated the effect of seasonal temperature variations (7-30 °C) on the H₂S removal performance of a biotrickling filter system, with an effective H₂S elimination capacity of 98.1 g/m³/h (removal efficiency = 83.1 %) achieved at temperatures of 10-12 °C. Biofilm growth was found to be accelerated by increased secretion of extracellular polymeric substances, enhanced biofilm adhesion capacity and relatively high levels of elemental sulfur accumulation, which help to retain heat within the filter bed under cold conditions. High-throughput sequencing showed that the psychrotolerant sulfur-oxidizing bacterium (SOB) Metallibacterium was gradually enriched (54.8 %) at temperatures below 15 °C. The major pathways of sulfur metabolism under low temperature conditions were determined based on the detection of enzymes related to sulfur metabolism. Finally, a strategy to enrich Metallibacterium was proposed to promote the application of biodesulfurization under low temperature conditions.

Bacteriobiota of the Cave Church of Sts. Peter and Paul in Serbia-Culturable and Non-Culturable Communities' Assessment in the Bioconservation Potential of a Peculiar Fresco Painting

The principal aim of this study was to determine bacterial diversity within the Cave Church of Sts. Peter and Paul, via culturable and non-culturable approaches, and elucidate the antifungal potential of autochthonous antagonistic bacterial isolates against biodeteriogenic fungi. Furthermore, whole-genome sequencing of selected bacterial antagonists and the analysis of genes included in the synthesis of secondary metabolites were performed. With the highest RA values, determined in metabarcoding analysis, phyla Actinobacteriota (12.08-54.00%) and Proteobacteria (25.34-44.97%) dominated most of the samples. A total of 44 different species, out of 96 obtained isolates, were determined as part of the culturable bacteriobiota, with the predominance of species from the genus Bacillus. Bacillus simplex was the only isolated species simultaneously present in all investigated substrata within the church. The best antagonistic activity against 10 biodeteriogenic fungi was documented for Streptomyces anulatus, followed by Bacillus altitudinis, Chryseobacterium viscerum, and Streptomyces sp. with their highest PGI% values ranging of from 55.9% to 80.9%. These promising results indicate that characterized bacteria are excellent candidates for developing biocontrol strategies for suppressing deteriogenic fungi responsible for the deterioration of investigated fresco painting. Finally, isolate 11-11MM, characterized as Streptomyces sp., represents a new species for science prompting the need for further study.

Adding organics to enrich mixotrophic sulfur-oxidizing bacteria under extremely acidic conditions-A novel strategy to enhance hydrogen sulfide removal

Biotreatment of high load hydrogen sulfide (H2S) can lead to rapid acidification of a bioreactor, which greatly challenges the application of bio-desulfurization technology. In this study, the bio-desulfurization performance was improved by enriching acidophilic mixotrophic sulfur-oxidizing bacteria (SOB) by adding organics under extremely acidic conditions (pH < 1.0). A biotrickling filter (BTF) for the removal of H2S was established and operated under pH < 1.0 for 420 days. In the autotrophic period, the maximum H2S elimination capacity (ECmax-H2S) was 135.8 g/m3/h with biofilm mass remaining within 11.1 g/L-BTF. The autotrophic SOB bacterium Acidithiobacillus was dominant (62.1 %). When glucose was added to the BTF system, ECmax-H2S increased by 272 % to 464.3 g/m3/h as biofilm mass increased to 22.3 g/L-BTF. The acidophilic mixotrophic SOB bacteria Mycobacterium (78.4 %) and Alicyclobacillus (20.7 %) were enriched while Acidithiobacillus was gradually eliminated (<0.1 %). Furthermore, the major sulfur metabolism pathways were identified to explore the desulfurization mechanism under extremely acidic conditions. To maintain optimal desulfurization performance and avoid biofilm overgrowth in the BTF system, biofilm mass should be maintained within 20-22 g/L-BTF. This can be achieved by adding 1.0 g/L-BTF glucose every 20 days under a load rate of H2S in 50-90 g/m3/h and a trickling liquid velocity of 1.8 m/h. Extremely acidic conditions eliminated non-aciduric microorganisms so that the addition of organics can increase the abundance of acidophilic mixotrophic SOB (>99 %), thus offering a novel strategy for enhancing H2S removal.

Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times

Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.

Fungal Carbonyl Sulfide Hydrolase of Trichoderma harzianum Strain THIF08 and Its Relationship with Clade D β-Carbonic Anhydrases

Carbonyl sulfide (COS) is the most abundant and long-lived sulfur-containing gas in the atmosphere. Soil is the main sink of COS in the atmosphere and uptake is dominated by soil microorganisms; however, biochemical research has not yet been conducted on fungal COS degradation. COS hydrolase (COSase) was purified from Trichoderma harzianum strain THIF08, which degrades COS at concentrations higher than 10,000 parts per million by volume from atmospheric concentrations, and its gene cos (492 bp) was cloned. The recombinant protein purified from Escherichia coli expressing the cos gene converted COS to H₂S. The deduced amino acid sequence of COSase (163 amino acids) was assigned to clade D in the phylogenetic tree of the β-carbonic anhydrase (β-CA) family, to which prokaryotic COSase and its structurally related enzymes belong. However, the COSase of strain THIF08 differed from the previously known prokaryotic COSase and its related enzymes due to its low reactivity to CO₂ and inability to hydrolyze CS₂. Sequence comparisons of the active site amino acids of clade D β-CA family enzymes suggested that various Ascomycota, particularly Sordariomycetes and Eurotiomycetes, possess similar enzymes to the COSase of strain THIF08 with >80% identity. These fungal COSase were phylogenetically distant to prokaryotic clade D β-CA family enzymes. These results suggest that various ascomycetes containing COSase contribute to the uptake of COS by soil.

Pneumonia due to Mycobacterium cosmeticum in a renal transplant recipient

A 69-year-old man renal transplant recipient for 4 years, presented with 4-day history of cough and dyspnoea. He was diagnosed with community-acquired pneumonia and treated accordingly. He deteriorated requiring intensive care unit admission and intubation. Mycobacterial culture from bronchoalveolar lavage grew colonies within 7 days of incubation while Mycobacterium tuberculosis PCR was negative. The antibiotic regimen was adjusted to cover for rapidly growing mycobacteria with imipenem, amikacin and clarithromycin. The final culture reported Mycobacterium cosmeticum. He improved on the antibiotic regimen given which the organism turned to be sensitive to. We reported the second case with M. cosmeticum that fulfilled the diagnostic criteria for non-tuberculous mycobacterial lung infection. Improvement of patient’s lung infection on appropriate antibiotics points to a causal relationship.

Diversity of Biodeteriorative Bacterial and Fungal Consortia in Winter and Summer on Historical Sandstone of the Northern Pergola, Museum of King John III’s Palace at Wilanow, Poland

The aim of the presented investigation was to describe seasonal changes of microbial community composition in situ in different biocenoses on historical sandstone of the Northern Pergola in the Museum of King John III’s Palace at Wilanow (Poland). The microbial biodiversity was analyzed by the application of Illumina-based next-generation sequencing methods. The metabarcoding analysis allowed for detecting lichenized fungi taxa with the clear domination of two genera: Lecania and Rhinocladiella. It was also observed that, during winter, the richness of fungal communities increased in the biocenoses dominated by lichens and mosses. The metabarcoding analysis showed 34 bacterial genera, with a clear domination of Sphingomonas spp. across almost all biocenoses. Acidophilic bacteria from Acidobacteriaceae and Acetobacteraceae families were also identified, and the results showed that a significant number of bacterial strains isolated during the summer displayed the ability to acidification in contrast to strains isolated in winter, when a large number of isolates displayed alkalizing activity. Other bacteria capable of nitrogen fixation and hydrocarbon utilization (including aromatic hydrocarbons) as well as halophilic microorganisms were also found. The diversity of organisms in the biofilm ensures its stability throughout the year despite the differences recorded between winter and summer.

A Review on Sampling Techniques and Analytical Methods for Microbiota of Cultural Properties and Historical Architecture

World cultural heritage suffers from deterioration caused by both natural and anthropogenic processes, among which microorganisms are significantly involved. Among the key issues of this topic, sampling techniques and analytical methods for revealing the microbiome are fundamental to obtaining useful results for understanding the key players and processes involved, and also for effective protection and management of the cultural heritage for humanity. A non-invasive and non-destructive sampling method is required for sampling of cultural properties prior to further analysis of the microbiome. One example is illustrated in this article. For many years, culture-dependent methods had been used before the invention of polymerase-chain reaction (PCR) methods and, more recently, specifically high-throughput next generation sequencing (NGS). NGS reveals the whole microbial community composition and the active microorganisms from genomic DNA and RNA, respectively. The recovered environmental DNA and RNA from samples provide the information on microbial community and composition, and the active members and biochemical processes of the microbial attributes. It should be emphasized that the metabolically-active members of functional microflora in the biofilm or microbiome on cultural heritage must be determined and identified from the RNA-based analysis to gain a substantially important insight of the active biodeterioration processes and also the effectiveness of the conservation strategies. The importance of the culture-independent technique, based on NGS, is that it can be used in combination with the conventional culturing methods to guide the isolation and enrichment of new microorganisms to gain further biochemical insights to advance the role of the specific microbial groups for biodeterioration of cultural heritage. At the same time, effective restoration and maintenance strategies can be formulated for the protection of world cultural heritage.

Non-Tuberculous Mycobacteria: Molecular and Physiological Bases of Virulence and Adaptation to Ecological Niches

Non-tuberculous mycobacteria (NTM) are paradigmatic colonizers of the total environment, circulating at the interfaces of the atmosphere, lithosphere, hydrosphere, biosphere, and anthroposphere. Their striking adaptive ecology on the interconnection of multiple spheres results from the combination of several biological features related to their exclusive hydrophobic and lipid-rich impermeable cell wall, transcriptional regulation signatures, biofilm phenotype, and symbiosis with protozoa. This unique blend of traits is reviewed in this work, with highlights to the prodigious plasticity and persistence hallmarks of NTM in a wide diversity of environments, from extreme natural milieus to microniches in the human body. Knowledge on the taxonomy, evolution, and functional diversity of NTM is updated, as well as the molecular and physiological bases for environmental adaptation, tolerance to xenobiotics, and infection biology in the human and non-human host. The complex interplay between individual, species-specific and ecological niche traits contributing to NTM resilience across ecosystems are also explored. This work hinges current understandings of NTM, approaching their biology and heterogeneity from several angles and reinforcing the complexity of these microorganisms often associated with a multiplicity of diseases, including pulmonary, soft-tissue, or milliary. In addition to emphasizing the cornerstones of knowledge involving these bacteria, we identify research gaps that need to be addressed, stressing out the need for decision-makers to recognize NTM infection as a public health issue that has to be tackled, especially when considering an increasingly susceptible elderly and immunocompromised population in developed countries, as well as in low- or middle-income countries, where NTM infections are still highly misdiagnosed and neglected.

Microbial Biodeterioration of Cultural Heritage: Events, Colonization, and Analyses

Geochemical cycles result in the chemical, physical, and mineralogical modification of rocks, eventually leading to formation of soil. However, when the stones and rocks are a part of historic buildings and monuments, the effects are deleterious. In addition, microorganisms also colonize these monuments over a period of time, resulting in formation of biofilms; their metabolites lead to physical weakening and discoloration of stone eventually. This process, known as biodeterioration, leads to a significant loss of cultural heritage. For formulating effective conservation strategies to prevent biodeterioration and restore monuments, it is important to know which microorganisms are colonizing the substrate and the different energy sources they consume to sustain themselves. With this view in scope, this review focuses on studies that have attempted to understand the process of biodeterioration, the mechanisms by which they colonize and affect the monuments, the techniques used for assessment of biodeterioration, and conservation strategies that aim to preserve the original integrity of the monuments. This review also includes the "omics" technologies that have started playing a large role in elucidating the nature of microorganisms, and how they can play a role in hastening the formulation of effective conservation strategies.

Micobacterias no tuberculosas de sitios arqueológicos de México

Se examinaron varios edificios de nueve sitios arqueológicos en México para detectar la presencia de micobacterias y se pudieron aislar 45 cepas no tuberculosas. Se obtuvieron a partir de biopelículas usando medios selectivos con antibióticos y colorantes. Las cepas aisladas se determinaron como micobacterias mediante una PCR específica, posteriormente se identificaron con tres marcadores moleculares: genes rrs (16S rRNA), hsp65 y rpoB. Además se relacionaron los datos fisiográficos de las zonas arqueológicas estudiadas con el número de bacterias ácido alcohol resistentes mediante un análisis univariado de varianza. De las 45 cepas de micobacterias aisladas 21 correspondieron a Mycobacteroides chelonae; siete, M. abscessus; cinco, Mycolicibacterium flavescens; cuatro, Mycobacterium alvei; dos, M. fortuitum; y seis quedaron como Mycobacterium sp. La mayoría de las micobacteriasno tuberculosas(MNT) fueron aisladas de dos de las zonas arqueológicas: 25 de Guachimontones (Jalisco) y 13 de Atetelco (Estado de México). El análisis estadístico mostró que los factores ambientales como clima y la interacción temperatura-humedad-precipitación tuvieron una gran influencia en la presencia de este grupo bacteriano en las zonas arqueológicas.

Nutrient cycling potential within microbial communities on culturally important stoneworks

Previous studies on microbes associated with deterioration of cultural heritage (CH) stoneworks have revealed a diverse microbiota adapted to stresses such as low nutrients, aridity and high salinity, temperatures and radiation. However, the function of these pioneer microbial communities is still unclear. This study examines bacterial and archaeal diversity in exfoliated and dark encrustation sandstone from Portchester Castle (UK) by 16S rRNA and functional gene analyses. Bacterial and archaeal communities from the exfoliated sites were distinctly different from the dark encrustation. Detected genera were linked to extreme environmental conditions, various potential functional roles and degradation abilities. From these data it was possible to reconstruct almost complete nitrogen and sulfur cycles, as well as autotrophic carbon fixation and mineral transformation processes. Analysis of RNA showed that many of the detected genera in these nutrient cycles were probably active in situ. Thus, CH stonework microbial communities are highly diverse and potentially self-sustaining ecosystems capable of cycling carbon, nitrogen and sulfur as well as the stone biodeterioration processes that lead to alterations such as exfoliation and corrosion. These results highlight the importance of diversity and internal recycling capacity in the development of microbial communities in harsh and low energy systems.

A thiotrophic microbial community in an acidic brine lake in Northern Chile

The endorheic basins of the Northern Chilean Altiplano contain saline lakes and salt flats. Two of the salt flats, Gorbea and Ignorado, have high acidic brines. The causes of the local acidity have been attributed to the occurrence of volcanic native sulfur, the release of sulfuric acid by oxidation, and the low buffering capacity of the rocks in the area. Understanding the microbial community composition and available energy in this pristine ecosystem is relevant in determining the origin of the acidity and in supporting the rationale of conservation policies. Besides, a comparison between similar systems in Australia highlights key microbial components and specific ones associated with geological settings and environmental conditions. Sediment and water samples from the Salar de Gorbea were collected, physicochemical parameters measured and geochemical and molecular biological analyses performed. A low diversity microbial community was observed in brines and sediments dominated by Actinobacteria, Algae, Firmicutes and Proteobacteria. Most of the constituent genera have been reported to be either sulfur oxidizing microorganisms or ones having the potential for sulfur oxidation given available genomic data and information drawn from the literature on cultured relatives. In addition, a link between sulfur oxidation and carbon fixation was observed. In contrast, to acid mine drainage communities, Gorbea microbial diversity is mainly supported by chemolithoheterotrophic, facultative chemolithoautotrophic and oligotrophic sulfur oxidizing populations indicating that microbial activity should also be considered as a causative agent of local acidity.

Comparison of microbial communities across sections of a corroding sewer pipe and the effects of wastewater flooding

This study investigated the variation in microbially induced concrete corrosion communities at different circumferential locations of a real sewer pipe and the effects of a wastewater flooding event on the community. Three distinct microbial community groups were found in different corrosion samples. The physico-chemical properties of the corrosion layers and the microbial communities were distinct for the cross-sectional positions within the pipe, ie ceiling, wall and tidal zones. The microbial communities detected from the same positions in the pipe were consistent over the length of the pipe, as well as being consistent between the replicate pipes. The dominating ceiling communities were members of the bacterial orders Rhodospirillales, Acidithiobacillales, Actinomycetales, Xanthomonadales and Acidobacteriales. The wall communities were composed of members of the Xanthomonadales, Hydrogenophilales, Chromatiales and Sphingobacteriales. The tidal zones were dominated by eight bacterial and one archaeal order, with the common physiological trait of anaerobic metabolism. Sewage flooding within the sewer system did not change the tidal and wall communities, although the corrosion communities in ceiling samples were notably different, becoming more similar to the wall and tidal samples. This suggests that sewage flooding has a significant impact on the corrosion community in sewers.

The Ecology of Acidophilic Microorganisms in the Corroding Concrete Sewer Environment

Concrete corrosion is one of the most significant problems affecting valuable sewer infrastructure on a global scale. This problem occurs in the aerobic zone of the sewer, where a layer of surface corrosion develops on the exposed concrete and the surface pH is typically lowered from around 11–10 (pristine concrete) to pH 2–4. Acidophilic microorganisms become established as biofilms within the concrete corrosion layer and enhance the loss of concrete mass. Until recently, the acidophilic community was considered to comprise relatively few species of microorganisms, however, the biodiversity of the corrosion community is now recognized as being extensive and varying from different sewer environmental conditions. The diversity of acidophiles in the corrosion communities includes chemolithoautotrophs, chemolithoheterotrophs, and chemoorganoheterotrophs. The activity of these microorganisms is strongly affected by H₂S levels in the sewer gas phase, although CO₂, organic matter, and iron in the corrosion layer influence this acidic ecosystem. This paper briefly presents the conditions within the sewer that lead to the development of concrete corrosion in that environment. The review focuses on the acidophilic microorganisms detected in sewer corrosion environments, and then summarizes their proposed functions and physiology, especially in relation to the corrosion process. To our knowledge, this is the first review of acidophilic corrosion microbial communities, in which, the ecology and the environmental conditions (when available) are considered. Ecological studies of sewer corrosion are limited, however, where possible, we summarize the important metabolic functions of the different acidophilic species detected in sewer concrete corrosion layers. It is evident that microbial functions in the acidic sewer corrosion environment can be linked to those occurring in the analogous acidic environments of acid mine drainage and bioleaching.

Degradation of carbonyl sulfide by Actinomycetes and detection of clade D of β-class carbonic anhydrase

Carbonyl sulfide (COS) is an atmospheric trace gas and one of the sources of stratospheric aerosol contributing to climate change. Although one of the major sinks of COS is soil, the distribution of COS degradation ability among bacteria remains unclear. Seventeen out of 20 named bacteria belonging to Actinomycetales had COS degradation activity at mole fractions of 30 parts per million by volume (ppmv) COS. Dietzia maris NBRC 15801T and Mycobacterium sp. THI405 had the activity comparable to a chemolithoautotroph Thiobacillus thioparus THI115 that degrade COS by COS hydrolase for energy production. Among 12 bacteria manifesting rapid degradation at 30 ppmv COS, D. maris NBRC 15801T and Streptomyces ambofaciens NBRC 12836T degraded ambient COS (∼500 parts per trillion by volume). Geodermatophilus obscurus NBRC 13315T and Amycolatopsis orientalis NBRC 12806T increased COS concentrations. Moreover, six of eight COS-degrading bacteria isolated from soils had partial nucleotide sequences similar to that of the gene encoding clade D of β-class carbonic anhydrase, which included COS hydrolase. These results indicate the potential importance of Actinomycetes in the role of soils as sinks of atmospheric COS.

Degradation and emission of carbonyl sulfide, an atmospheric trace gas, by fungi isolated from forest soil

Soil is thought to be important both as a source and a sink of carbonyl sulfide (COS) in the troposphere, but the mechanism affecting COS uptake, especially for fungi, remains uncertain. Fungal isolates that were collected randomly from forest soil showed COS-degrading ability at high frequencies: 38 out of 43 isolates grown on potato dextrose agar showed degradation of 30 ppmv COS within 24 h. Of these isolates, eight degraded 30 ppmv of COS to below the detection limit within 2 h. These isolates also showed an ability to degrade COS included in ambient air (around 500 pptv) and highly concentrated (12 500 ppmv) level, even though the latter is higher than the lethal level for mammals. COS-degrading activity was estimated by using ergosterol as a biomass index for fungi. Trichoderma sp. THIF08 had the highest COS-degrading activity of all the isolates. Interestingly, Umbelopsis/Mortierella spp. THIF09 and THIF13 were unable to degrade 30 ppmv COS within 24 h, and actually emitted COS during the cultivation in ambient air. These results indicate a fungal contribution to the flux of COS between the terrestrial and atmospheric environments.

Carbon dioxide and hydrogen sulfide associations with regional bacterial diversity patterns in microbially induced concrete corrosion

The microbial communities associated with deteriorating concrete corrosion fronts were characterized in 35 samples taken from wastewater collection and treatment systems in ten utilities. Bacterial communities were described using Illumina MiSeq sequencing of the V1V2 region of the small subunit ribosomal ribonucleic acid (SSU-rRNA) gene recovered from fresh corrosion products. Headspace gas concentrations (hydrogen sulfide, carbon dioxide, and methane), pore water pH, moisture content, and select mineralogy were tested for correlation to community outcomes and corrosion extent using pairwise linear regressions and canonical correspondence analysis. Corroding concrete was most commonly characterized by moisture contents greater than 10%, pore water pH below one, and limited richness (<10 taxa). Bacterial community composition was not correlated to geographic location when considered independently from other environmental factors. Corrosion was most severe in sites with high levels of hydrogen sulfide (>100 ppm) and carbon dioxide (>1%) gases, conditions which also were associated with low diversity biofilms dominated by members of the acidophilic sulfur-oxidizer genus Acidithiobacillus.

Draft Genome Sequence of Mycobacterium cosmeticum DSM 44829

We announce the draft genome sequence of Mycobacterium cosmeticum strain DSM 44829, a nontuberculous species responsible for opportunistic infection. The genome described here is composed of 6,462,090 bp, with a G+C content of 68.24%. It contains 6,281 protein-coding genes and 75 predicted RNA genes.

Bacterial communities in pigmented biofilms formed on the sandstone bas-relief walls of the Bayon Temple, Angkor Thom, Cambodia

The Bayon temple in Angkor Thom, Cambodia has shown serious deterioration and is subject to the formation of various pigmented biofilms. Because biofilms are damaging the bas-reliefs, low reliefs engraved on the surface of sandstone, information about the microbial community within them is indispensable to control biofilm colonization. PCR-denaturing gradient gel electrophoresis (DGGE) analysis of biofilm samples from the pigmented sandstone surfaces showed that the bacterial community members in the biofilms differed clearly from those in the air and had low sequence similarity to database sequences. Non-destructive sampling of biofilm revealed novel bacterial groups of predominantly Rubrobacter in salmon pink biofilm, Cyanobacteria in chrome green biofilm, Cyanobacteria and Chloroflexi in signal violet biofilm, Chloroflexi in black gray biofilm, and Deinococcus-Thermus, Cyanobacteria, and Rubrobacter in blue green biofilm. Serial peeling-off of a thick biofilm by layers with adhesive sheets revealed a stratified structure: the blue-green biofilm, around which there was serious deterioration, was very rich in Cyanobacteria near the surface and Chloroflexi in deep layer below. Nitrate ion concentrations were high in the blue-green biofilm. The characteristic distribution of bacteria at different biofilm depths provides valuable information on not only the biofilm formation process but also the sandstone weathering process in the tropics.

High-throughput amplicon sequencing reveals distinct communities within a corroding concrete sewer system

Microbially induced concrete corrosion (MICC) is an important problem in sewers. Here, small-subunit (SSU) rRNA gene amplicon pyrosequencing was used to characterize MICC communities. Microbial community composition differed between wall- and ceiling-associated MICC layers. Acidithiobacillus spp. were present at low abundances, and the communities were dominated by other sulfur-oxidizing-associated lineages.