Editorial: Microbial Taxonomy, Phylogeny and Biodiversity

The great diversity of microbial life is the remaining majorreservoir of unknown biologicaldiversity on Earth. To understand this vast, but largely unperceived diversity with its untappedgenetic, enzymatic and industrial potential, microbial systematics is undergoing a revolutionarychange in its approach to describe novel taxa based on genomic/envirogenomic information(Rosselló-Móra and Whitman, 2019)S

From the Gene Sequence to the Phylogeography through the Population Structure: The Cases of Yersinia ruckeri and Vibrio tapetis

Multilocus sequence analysis (MLSA) and multilocus sequence typing (MLST) are nowadays considered as gold standards in the study of microbial systematic, being both techniques based on the interpretation of the sequences of several housekeeping genes. In this context, the sequences can be analyzed from different points of view. On the one hand, the phylogeny of the bacterial species can be estimated using the MLSA approach and on the other hand, the structure of the population can be inferred by means of MLST. Moreover, most species display some degree of population structure that can be interpreted in geographic and chronological contexts, that is, phylogeographic studies. In this review, the phylogeny and population structure of two important fish and shellfish pathogens, Yersinia ruckeri and Vibrio tapetis, exhibiting very different evolutive patterns will be analyzed. In both cases, the species form robust and monophyletic groups from a phylogenetic point of view. Regarding to the population structure, very different results were found. While Y. ruckeri follows an epidemic model of clonal expansion with well‐adapted clones that explode to be widely distributed, V. tapetis appears to have a mixed structure in where the paradox of clonality and high level of variability coexist. Furthermore, phylogeographical studies provided the evolutionary and geographical context for the species, allowing the determination of historical and spatial influences on the diversification of both species

How efficiently does a metabolically enhanced system with denitrifying anaerobic methane oxidizing microorganisms remove antibiotics?

In this work, the novel N-damo (Nitrite dependent anaerobic methane oxidation) process was investigated at high biomass activities for its potential to remove simultaneously nitrite and methane, as well as selected antibiotics commonly found in sewage in trace amounts. For this purpose, two MBRs were operated at three high nitrite loading rates (NLRs), namely 76 ± 9.9, 161.5 ± 11.4 and 215.2 ± 24.2 mg N–NO⁻2 L−1 d−1, at long-term operation. The MBRs performance achieved a significantly high nitrite removal activity for an N-damo process (specific denitrifying activity of up to 540 mg N–NO⁻2 g−1 VSS d−1), even comparable to heterotrophic denitrification values. In this study, we have implemented a novel operational strategy that sets our work apart from previous studies with similar bioreactors. Specifically, we have introduced Cerium as a trace element in the feeding medium, which serves as a key differentiating factor. It allowed maintaining a stable reactor operation at high NLRs. Microbial community composition evidenced that both MBRs were dominated with N-damo bacteria (67–87% relative abundance in period III and I, respectively). However, a decrease in functional N-damo bacteria (Candidatus Methylomirabilis) abundance was observed during the increase in biomass activity and concentration, concomitantly with an increase of the other minor families (Hypomicrobiaceae and Xanthobacteraceae). Most of the selected antibiotics showed high biotransformation such as sulfamethoxazole, trimethoprim, cefalexin and azithromycin, whereas others such as roxithromycin and clarithromycin were only partially degraded (20–35%). On the contrary, ciprofloxacin showed almost no removal. Despite the metabolic enhancement, no apparent increase on the antibiotic removal was observed throughout the operation, suggesting that microbiological composition was of greater influence than its primary metabolic activity on the removal of antibioticsThis research was supported by the European Union's Horizon 2020 research and innovation programme under the project NOWELTIES, through the Marie Sklodowska-Curie grant agreement 812880, as well as the Ministry of Economy and Competitiveness, Spain through ANTARES (PID 2019-110346RB-C21) project. Authors belong to CRETUS Strategic Partnership (AGRUP 2015/02) and to Galician Competitive Research Group (GRC ED431C-2021/37)S

Thermal hydrolysis pre-treatment has no positive influence on volatile fatty acids production from sewage sludge

The study compares the potential to produce volatile fatty acids (VFA) from sewage sludge, both raw and thermally pre-treated in two modes of operation. In batch mode, raw sludge at pH 8 obtained the highest maximum VFA yield (0.41 g COD-VFA/g CODfed) whereas pre-treated sludge achieved a lower value (0.27 g COD-VFA/g CODfed). The operation of 5-L continuous reactors showed that thermal hydrolysis pre-treatment (THP) did not have any significant influence on VFA yields, averaging 15.1 % g COD-VFA/g COD with raw sludge and 16.6 % g COD-VFA/g COD with pre-treated one. Microbial community analysis showed that phylum Firmicutes was predominant in both reactors and that the enzymatic profiles involved in VFA production were very similar regardless of the substrate fedThis work is part of the ECOVAL and CIGAT CIRCULAR projects, which are funded by Interreg Sudoe (SOE4/P1/E1104) and by the Xunta de Galicia and Viaqua (IN853C2022/03), respectively. Juan M. Lema belongs to the Galician competitive research group ED431C-2021/37 co-funded by Xunta de Galicia and ERDF (EU)S

Influence of metabolism and microbiology on organic micropollutants biotransformation in anoxic heterotrophic reactors

There is scarce information about the biotransformation of organic micropollutants (OMPs) under anoxic conditions. In this study, a heterotrophic denitrifying bioreactor was set up to study the fate of several OMPs from metabolic and microbiological points of view. Primary metabolic activity was increased by adding progressively higher nitrogen loading rates during the operation (from 0.075 to 0.4 g N-NO3- L−1 d−1), which resulted in an important shift in the microbial population from a specialized biomass to a more diverse community. Such a change provoked a significant increase in the removal efficiency of erythromycin (ERY), roxithromycin (ROX) and bisphenol-A (BPA), and some bacterial taxa, such as Rhodoplanes, were identified as possible indicators related to the biodegradation of these compounds. The increasing primary metabolic activity in the reactor did not enhance the OMP-specific removal rates, suggesting that the bacterial composition is more influential than cometabolismThis research was supported by the Spanish Research State Agency (AEI) through ANTARES (PID2019–110346RB-C21) project. M. Martinez-Quintela would also like to express his gratitude to the same agency for awarding a research scholarship (BES-2017–080503). All authors belong to the Galician Competitive Research Groups (GRC)_ ED431C-2021/37S

Study of the microbiota associated to Ruditapes decussatus and Ruditapes philippinarum clams by 16S rRNA metabarcoding, dilution to extinction, and culture-based techniques

The study of the microbiota associated to clams is important not only to know their sanitary status but also to prevent pathobiology events. The use of different microbiological techniques can help to obtain a better picture of the bacterial diversity of clams as well as to isolate new bacterial taxa. In this study, two clam species, Ruditapes decussatus and R. philippinarum, were analyzed in two locations of Galicia (northwest of Spain) in April and October, by combining classic culturing, dilution-to-extinction approach, and 16S rRNA gene target sequencing. 16S rRNA gene target sequencing revealed a great diversity within the clam samples, shedding light into the vast microbial communities associated to these bivalves. All samples were dominated by the same bacterial genera in the different periods, namely Mycoplasma, Vibrio, and Cutibacterium. The α-diversity in the samples obtained during the month of October was lower and showed the dominance of rare bacterial taxa, such as Methylobacterium or Psychrobacter. Dilution-to-extinction technique demonstrated its usefulness to culture rare bacterial taxa that were not found in clams under the classic culturing techniques, including Rahnella, Brachybacterium, Micrococcus, Jantinobacter, and Lelliottia. Altogether, our study provides valuable information on the microbiota associated to R. decussatus and R. philippinarum, demonstrating the high complexity and dynamics of these microbial populationsOpen Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This work was supported in part by grant AGL2013-42628-R and AGL2016-77539-R from the Ministerio de Economía y Competitividad (Spain)S

Sulfamethoxazole enhances specific enzymatic activities under aerobic heterotrophic conditions: a metaproteomic approach

The growing concern about antibiotic-resistant microorganisms has focused on the sludge from wastewater treatment plants (WWTPs) as a potential hotspot for their development and spread. To this end, it seems relevant to analyze the changes on the microbiota as a consequence of the antibiotics that wastewater may contain. This study aims at determining whether the presence of sulfamethoxazole (SMX), even in relatively low concentrations, modifies the microbial activities and the enzymatic expression of an activated sludge under aerobic heterotrophic conditions. For that purpose, we applied a metaproteomic approach in combination with genomic and transformation product analyses. SMX was biotransformed, and the metabolite 2,4(1H,3H)-pteridinedione-SMX (PtO-SMX) from the pterin-conjugation pathway was detected at all concentrations tested. Metaproteomics showed that SMX at 50–2000 μg/L slightly affected the microbial community structure, which was confirmed by DNA metabarcoding. Interestingly, an enhanced activity of the genus Corynebacterium and specifically of five enzymes involved in its central carbon metabolism was found at increased SMX concentrations. Our results suggest a role of Corynebacterium genus on SMX risks mitigation in our bioreactorsThis research was funded by the Spanish Government (Agencia Estatal de Investigación) through the ANTARES project (PID2019-110346RB-C21), a PhD Xunta de Galicia Grant (ED481A-2018/113, D.M.K.-V.) and a Juan de la Cierva-Formación postdoctoral grant (FJC2019-041664-I, A.T.-S.). The authors belong to the Galician Competitive Research Groups (GRC_ ED431C-2021/37)S

Revisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos

Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA–DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species ‘A. aquaticus’ appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment. The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate ‘Arcomarinus’ gen. nov. are proposedThis work was supported in part by Grants JPIW2013-69095-C03-03 from the Ministerio de Economía y Competitividad (MINECO), AQUAVALENS of the Seventh Framework Program (FP7/2007-2013) grant agreement 311846 from the European Union and AGL2013-42628-R and AGL2016-77539-R (AEI/FEDER UE) from the Agencia Estatal de Investigación (Spain)S

The fate of SARS-COV-2 in WWTPS points out the sludge line as a suitable spot for detection of COVID- 19

SARS-CoV-2 genetic material is detectable in the faeces of a considerable part of COVID-19 cases and hence, in municipal wastewater. This fact was confirmed early during the spread of the COVID-19 pandemic and prompted several studies that proposed monitoring its incidence by wastewater. This paper studies the fate of SARS-CoV-2 genetic material in wastewater treatment plants using RT-qPCR with a two-fold goal: i) to check its presence in the water effluent and in the produced sludge and ii) based on the understanding of the virus particles fate, to identify the most suitable spots for detecting the incidence of COVID-19 and monitor its evolution. On the grounds of the affinity of enveloped virus towards biosolids, we hypothesized that the sludge line acts as a concentrator of SARS-CoV-2 genetic material. Sampling several spots in primary, secondary and sludge treatment at the Ourense (Spain) WWTP in 5 different days showed that, in effect, most of SARS-CoV-2 particles cannot be detected in the water effluent as they are retained by the sludge line. We identified the sludge thickener as a suitable spot for detecting SARS-CoV-2 particles thanks to its higher solids concentration (more virus particles) and longer residence time (less sensitive to dilution caused by precipitation). These findings could be useful to develop a suitable strategy for early warning of COVID-19 incidence based on WWTP monitoringSabela Balboa, Miguel Mauricio-Iglesias and Juan M. Lema belong the following programs co-funded by ERDF (EU): the CRETUS Strategic Partnership (ED431E 2018/01) and the Galician Competitive Research Group (ED431C2017/029)S

Biologic Therapy for Moderate to Severe Psoriasis. Real-World Follow-up of Patients Who Initiated Biologic Therapy at Least 10 Years Ago

[Abstract] Introduction: The aim of this study was to evaluate response and drug survival of biologic therapy in patients with moderate to severe plaque-type psoriasis who initiated biologic therapy at least 10 years ago, in a real-world setting. Methods: This was an observational retrospective follow-up study that included patients with moderate to severe plaque-type psoriasis who initiated biologic therapy between October 2006 and December 2009. Efficacy was expressed as the percentage of patients achieving a 50, 75 and 90% reduction from baseline in the Psoriasis Area and Severity Index (PASI 50, PASI 75, PASI 90, respectively) every 3 months during the first year of therapy and then every 12 months up to the end of follow-up or withdrawal from the study. Results: A total of 56 patients were included in the study, representing 140 treatment lines (median 2, range 1-8); of these patients, 53 were still receiving biologic therapy at the end of the study. The mean duration of biologic therapy was 140.4 (range 47.6-175.4) months. Etanercept was used in 98.2% of patients, followed by efalizumab (42.9%), adalimumab (41.1%), ustekinumab (33.9%) and infliximab (16.1%). Treatment lines were switched in 62.1% of treatments: 24.3% due to secondary failure, 20.7% due to primary failure and 3.6% due to side effects. No patient treated with anti-interleukins had to discontinue treatment due to side effects. Ustekinumab had the highest drug survival. Conclusions: This study in the real-world-setting shows maintenance of long-term efficacy and safety of biologic therapy in patients with moderate to severe plaque psoriasis in daily practice who initiated biologic therapy 10 years ago.The journal’s Rapid Service Fee was paid for by Fundación Profesor Novoa Santos (A Coruña. Spain