Analysis of Biodeteriogens on Architectural Heritage. An Approach of Applied Botany on a Gothic Building in Southern Italy

The degradation of stone materials depends on several interlinked factors. The effects caused by biodeteriogens on mineral-based substrates are now increasingly considered in the field of cultural heritage conservation from different experimental approaches. In this study, biodeteriogenic micro- and macroflora within the gothic building of Santa Maria della Pietà, Squillace, Calabria, have been analyzed using multiple approaches, such as optical microscopy and molecular techniques. All 17 plant species detected are usually widespread in Mediterranean regions and some of these, such as Ailanthus altissima and Ficus carica, showed a very high hazard index, which is potentially dangerous for masonry stability. Fungi, cyanobacteria, and green algae were identified within biofilm compositions in a total of 23 different taxa, showing many similarities with microbial associations commonly found in cave and hypogean environments. All of the 11 fungal taxa detected belong to Ascomycota phylum, with Penicillium as the most represented genus. Photoautotrophic organisms are mostly represented by filamentous genera, with widespread presence of Leptolyngbya as the most abundant genus. The results highlighted how the singular environmental conditions of the study site, combined with the architectural features and the building materials, determined all the degradation phenomena affecting the building’s internal surfaces, compromising over time the structural integrity.

Comparison of the airway microbiota in children with chronic suppurative lung disease

RationaleThe airway microbiota is important in chronic suppurative lung diseases, such as primary ciliary dyskinesia (PCD) and cystic fibrosis (CF). This comparison has not previously been described but is important because difference between the two diseases may relate to the differing prognoses and lead to pathological insights and potentially, new treatments.ObjectivesTo compare the longitudinal development of the airway microbiota in children with PCD to that of CF and relate this to age and clinical status.MethodsSixty-two age-matched children (age range 0.5–17 years) with PCD or CF (n=31 in each group) were recruited prospectively and followed for 1.1 years. Throat swabs or sputum as well as clinical information were collected at routine clinical appointments. 16S rRNA gene sequencing was performed.Measurements and main resultsThe microbiota was highly individual and more diverse in PCD and differed in community composition when compared with CF. While Streptococcus was the most abundant genus in both conditions, Pseudomonas was more abundant in CF with Haemophilus more abundant in PCD (Padj=0.0005). In PCD only, an inverse relationship was seen in the relative abundance of Streptococcus and Haemophilus with age.ConclusionsBacterial community composition differs between children with PCD and those with CF. Pseudomonas is more prevalent in CF and Haemophilus in PCD, at least until infection with Pseudomonas supervenes. Interactions between organisms, particularly members of Haemophilus, Streptococcus and Pseudomonas genera appear important. Study of the interactions between these organisms may lead to new therapies or risk stratification.

Understanding the Role of Prevotella Genus in the Digestion of Lignocellulose and Other Substrates in Vietnamese Native Goats’ Rumen by Metagenomic Deep Sequencing

Bacteria in rumen play pivotal roles in the digestion of nutrients to support energy for the host. In this study, metagenomic deep sequencing of bacterial metagenome extracted from the goats’ rumen generated 48.66 GB of data with 3,411,867 contigs and 5,367,270 genes. The genes were mainly functionally annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) Carbohydrate-Active enZYmes (CAZy), and HMMER database, and taxonomically classified by MEGAN. As a result, 65,554 genes encoding for 30 enzymes/proteins related to lignocellulose conversion were exploited, in which nine enzymes were seen for the first time in goat rumen. Prevotella was the most abundant genus, contributing 30% hemicellulases and 36% enzymes/proteins for lignocellulose pretreatment, and supporting 98.8% of feruloyl esterases and 71.7% acetylxylan esterases. In addition, 18 of the 22 most lignocellulose digesting- potential contigs belonged to Prevotella. Besides, Prevotella possessed many genes coding for amylolytic enzymes. One gene encoding for endoxylanase was successfully expressed in E. coli. The recombinant enzyme had high Vmax, was tolerant to some salts and detergents, worked better at pH 5.5–6.5, temperature 40–50 °C, and was capable to be used in practices. Based on these findings, we confirm that Prevotella plays a pivotal role for hemicellulose digestion and significantly participates in starch, cellulose, hemicellulose, and pectin digestion in the goat rumen.

Effect of Enterococcus faecium as a Water and/or Feed Additive on the Gut Microbiota, Hematologic and Immunological Parameters, and Resistance Against Francisellosis and Streptococcosis in Nile Tilapia (Oreochromis niloticus)

In the present study, we evaluated the effects of administering Enterococcus faecium in food and/or water on the hematological and immunological parameters, intestinal microbiota, resistance to bacterial diseases (streptococcosis and francisellosis) and growth of Nile tilapia. Before the in vivo experiment, probiotic bacteria isolated from Nile tilapia were selected via inhibition tests. Sequencing, annotation, and assembly of the complete genome of the selected bacteria as well as other tests were performed using bioinformatics tools. Three treatments were implemented: G1 (probiotic feeding), G2 (probiotic in water), and G3 (probiotic in food and water); and a negative control (NC) was also employed. Treatment lasted 38 days, and each group consisted of fish and two repetitions. The fish were divided and infected with Streptococcus agalactiae S13 (serotype Ib) and Francisella orientalis. The G1 group had a higher average final weight gain than the G2, G3, and NC groups. Further, a significant increase in the number of thrombocytes was observed in the groups administered probiotics in the diet (G1 and G3). A statistical difference was observed in the mortality of fish infected with S. agalactiae in the NC compared to the treated groups. Cetobacterium was the 43 most abundant genus in the intestinal microbiota of all groups, including the NC group. E. faecium increased the immunity of fish administered the treatment and decreased the mortality caused by S. agalactiae. As an autochtone probiotic, E. faecium does not interfere with the local ecosystem and thus has a great probiotic potential for Nile tilapia in Brazil.

Exploration of microbial communities contributing to effective methane production from scum under anaerobic digestion

Scum is formed by the adsorption of long-chain fatty acids (LCFAs) onto biomass surface in anaerobic digestion of oily substrates. Since scum is a recalcitrant substrate to be digested, it is disposed via landfilling or incineration, which results in biomass washout and a decrease in methane yield. The microbes contributing to scum degradation are unclear. This study aimed to investigate the cardinal microorganisms in anaerobic scum digestion. We pre-incubated a sludge with scum to enrich scum-degrading microbes. Using this sludge, a 1.3-times higher methane conversion rate (73%) and a faster LCFA degradation compared with control sludge were attained. Then, we analyzed the cardinal scum-degrading microbes in this pre-incubated sludge by changing the initial scum-loading rates. Increased 16S rRNA copy numbers for the syntrophic fatty-acid degrader Syntrophomonas and hydrogenotrophic methanogens were observed in scum high-loaded samples. 16S rRNA amplicon sequencing indicated that Syntrophomonas was the most abundant genus in all the samples. The amino-acid degrader Aminobacterium and hydrolytic genera such as Defluviitoga and Sporanaerobacter became more dominant as the scum-loading rate increased. Moreover, phylogenic analysis on Syntrophomonas revealed that Syntrophomonas palmitatica, which is capable of degrading LCFAs, related species became more dominant as the scum-loading rate increased. These results indicate that a variety of microorganisms that degrade LCFAs, proteins, and sugars are involved in effective scum degradation.

Succession of Fungal Communities at Different Developmental Stages of Cabernet Sauvignon Grapes From an Organic Vineyard in Xinjiang

Fungi present on grape surface considerably impact grape growth and quality. However, information of the fungal community structures and dynamics on the worldwide cash crop, the Cabernet Sauvignon grape, from the budding to ripening stages remains limited. Here, we investigated the succession of fungal communities on Cabernet Sauvignon grapes from an organic vineyard in Xinjiang, China at different developmental stages via high-throughput sequencing combined with multivariate data analysis. In total, 439 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal communities differed over the budding to the berry stages. Moreover, Aspergillus, Malassezia, Metschnikowia, and Udeniomyces were predominant during the unripe stage, whereas Erysiphe, Cryptococcus, Vishniacozyma, and Cladosporium were dominant in the ripe stages. Notably, Vishniacozyma was the most abundant genus, conserved in all development stages. Moreover, network analysis resulted in 171 edges—96 negative and 75 positive. Moreover, fungal genera such as Vishniacozyma, Sporobolomyces, Aspergillus, Alternaria, Erysiphe, Toxicodendron, and Metschnikowia were present in the hubs serving as the main connecting nodes. Extensive mutualistic interactions potentially occur among the fungi on the grape surface. In conclusion, the current study expounded the characteristics of the Cabernet Sauvignon grape fungal community during the plant growth process, and the results provided essential insights into the potential impacts of fungal communities on grape growth and health.

Effects of Rhizosphere Microbial Composition on the Growth of Cajanus Cajan in Coal Gangue Reclaimed Soil

Planting the economically sustainable Cajanus cajan crop in coal gangue dump as an approach for ecological management has attracted extensive attention from scholars worldwide. Microorganisms play important roles in ecological restoration. However, there have been few reports about the microbial composition and functions of Cajanus cajan root systems planted in plateau waste dumps. In this study, the gangue dump (1,390 m above sea level) in Guizhou Plateau was covered with soil and planted with YN and JX Cajanus cajans. After one year, the Cajanus cajan root system was collected, and high-throughput sequencing was utilized to examine the bacterial and fungal biodiversity. The bacteria in all samples were assigned to six phyla and 60 genera. The unclassified_f_Enterobacteriaceae and Cedecea were the most abundant genera. The fungi were assigned to six phyla and 143 genera and Fusarium was the most abundant genus. Venn and heatmap analyses revealed differences in the dominant root species among Cajanus cajan varieties, Lactococcus and Fusarium. In JX and YN, Pseudoarthrobacter is a unique genus of bacteria; in JX, Robillarda is a unique genus of fungi; and in YN, Scytalidium is a unique genus of fungi. The endophytic fungi mainly play the roles of saprotroph, plant pathogen, and endophyte. Among the bacterial properties, L-arabinose isomerase and adenosine triphosphatase were the most abundant in all samples, while chitinase, catalase, and laccase played important roles in photosynthesis, degradation of lignin, chitin, and chitosan. This study guides the selection of reclamation plants and strategies for the migration and restriction of heavy metals in soil.

Bacterial Diversity of Breast Milk in Healthy Spanish Women: Evolution from Birth to Five Years Postpartum

The objective of this work was to characterize the microbiota of breast milk in healthy Spanish mothers and to investigate the effects of lactation time on its diversity. A total of ninety-nine human milk samples were collected from healthy Spanish women and were assessed by means of next-generation sequencing of 16S rRNA amplicons and by qPCR. Firmicutes was the most abundant phylum, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. Accordingly, Streptococcus was the most abundant genus. Lactation time showed a strong influence in milk microbiota, positively correlating with Actinobacteria and Bacteroidetes, while Firmicutes was relatively constant over lactation. 16S rRNA amplicon sequencing showed that the highest alpha-diversity was found in samples of prolonged lactation, along with wider differences between individuals. As for milk nutrients, calcium, magnesium, and selenium levels were potentially associated with Streptococcus and Staphylococcus abundance. Additionally, Proteobacteria was positively correlated with docosahexaenoic acid (DHA) levels in breast milk, and Staphylococcus with conjugated linoleic acid. Conversely, Streptococcus and trans-palmitoleic acid showed a negative association. Other factors such as maternal body mass index or diet also showed an influence on the structure of these microbial communities. Overall, human milk in Spanish mothers appeared to be a complex niche shaped by host factors and by its own nutrients, increasing in diversity over time.

Comparative Analysis of Traditional and Modern Fermentation for Xuecai and Correlations Between Volatile Flavor Compounds and Bacterial Community

Differences in flavor compounds and bacterial communities of Xuecai by traditional and modern fermentation are poorly understood. Allyl isothiocyanate (E9), ethyl acetate (E1), 3-butenenitrile (N1), phenol (P1), ethanol (A1), and 3-(2,6,6-trimethyl-1-cyclohexen-1-yl) acrylaldehyde (L11) were the main flavor compounds that differed between Xuecai produced by traditional and modern fermentation. Among these compounds, the contents of N1 and E9 were higher in modern fermentation Xuecai. Traditional fermentation Xuecai possessed higher contents of A1, P1, E1, and L11. High-throughput sequencing showed that Lactobacillus-related genera was the most abundant genus (50%) in modern fermentation Xuecai. However, in traditional fermentation Xuecai, Halanaerobium (29.06%) and Halomonas (12.96%) were the dominant genera. Halophilic bacteria (HB) positively contribute to the flavor of Xuecai. Carbohydrate metabolism and amino acid metabolism were the most abundant pathways associated with the bacterial communities of the Xuecai. This indicated that Xuecai flavor formation is mainly dependent on protein and carbohydrate degradation. This study provides a novel insight that HB may be important for flavor formation of Xuecai.

Effect of organic loading on phosphorus forms transformation and microbial community in continuous-flow A2/O process

A continuous-flow Anaerobic/Anoxic/Oxic (A2/O) system was operated at different organic concentrations to systematically investigate the effect on the nutrient removal, secretion characteristics of extracellular polymer, phosphorus forms transformation and changes in functional flora in this system. The results showed that high organic loading was more conducive to promote the secretion of extracellular polymeric substance (EPS), the increase of polysaccharide content was more obvious compared with protein, the impact of organic loading on the components of loosely-bound EPS (LB-EPS) was higher than that of tight-bound EPS (TB-EPS). Phosphorus in sludge floc mainly existed in the form of inorganic phosphorus (IP), and IP mainly existed in the form of apatite inorganic phosphorus (AP). High organic load showed higher phosphorus storage in EPS, and the phosphorus content in EPS was positively correlated with the content of EPS. Non-apatite phosphorus (NAIP) content played an important role in the extracellular dephosphorization. The abundance of Nitrosomonas and Nitrospira responsible for nitrification decreased with the increase of organic loading. The group of denitrifiers was large, and Azospira was the most abundant genus among them. Dechloromonas, Acinetobacter, Povalibacter, Chryseolinea and Pirellula were the functional genera closely associated with phosphorus removal.