Functional redundancy is a mechanism that guarantees the maintenance of ecological processes that are crucial to the functionality of the ecosystem, even with the loss of species. Although widely studied in animals and plants, little is understood about the functional redundancy in microbial communities despite the importance of these communities for the maintenance of numerous ecosystem services. Rare microorganisms, microbial taxa with relative abundance below 0.01%, play a key role in maintaining ecosystem services, but are generally neglected in studies of functional redundancy in microbial communities. In the present study, we collected 6794 metagenomic samples, obtained from 73 habitats distributed in 9 ecosystems across the planet, from which we calculated the functional redundancy in microbial communities from different ecosystems. To test the relationship between relative abundance and richness of the rare biosphere of the microorganism community and the functional redundancy indices found, we performed a simple linear regression considering significant the analyzes whose P value <0.05. Our findings demonstrate that functional redundancy differs considerably between the studied ecosystems. Data from this study reveal that the functional redundancy of microbial communities is apparently strongly influenced by the lifestyle of microorganisms and the environments in which they are inserted. The analysis carried out revealed that microbial communities with a high richness of rare microorganisms generally have reduced functional redundancy which leads us to believe that rare microorganisms can be important in performing highly specialized and distinct functions in each environment and their extinction can trigger cascading effects reducing the functionality of ecosystems.

SARS-COV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) is the virus that causesCOVID-19 (Coronavirus Disease 2019). The reach and negative impact of SARS-CoV-2across the world has placed this pandemic among the most notorious on record. Because it isa global emergency, as well as the growing number of cases and deaths caused and thecharacteristics of SARS-CoV-2, such as the high transmissibility between individuals and thevariability of clinical manifestations associated with the infection, make laboratory diagnosisa tool very important in the fight against the pandemic. Epidemiological screening for SARS-CoV-2 aims to correctly identify patients exposed to the virus to better understand theprevalence, epidemiology and dynamics of the disease. There is a lot to understand about theinteraction between SARS-CoV-2 and its host. With this, the search for a betterunderstanding of the immunological aspects of SARS-CoV-2 has increased. Thus, understanding how the antibody response works during and after natural infection is essentialto better understand the disease, as well as evaluating the immune response induced by thevaccine to understand how the antibody response works during and after infection. In thissense, a long-term follow-up study is important to understand, monitor and investigate IgGantibody levels. This study aimed to evaluate the level of antibodies to SARS-CoV-2 ingroups of infected patients (previously tested by qRT-PCR with detectable results for SARS-CoV2) and subsequently vaccinated in Salvador, Bahia, Brazil. For this, serologicalcollections were carried out from 245 individuals, where six analyzes of the presence ofantibodies of the IgG class were carried out through the enzyme-linked immunoabsorptiontest (ELISA) in the serum samples of these individuals over approximately 1 year, at differenttimes in the Virology Laboratory of the Federal University of Bahia - UFBA. In this work, itis learned that primary vaccination induced a significant increase in SARS-CoV-2 specificantibodies, which was further intensified by the booster dose. However, in individualsrecovered from SARS-CoV2, there was no further increase in antibody levels after thesecond vaccine dose. Notably, IgG levels were similar in individuals who were not infectedwith SARS-CoV-2 and in individuals who recovered from SARS-CoV-2 after a booster dose.

Probiotics are microorganisms with beneficial properties for the health of the host who consumes them. These can be applied both in industry and in the promotion of human health, such as for the treatment of inflammatory bowel diseases. Currently, it is possible to find several studies on lactobacilli, especially Lactiplantibacillus plantarum, however, due to its great genetic diversity, the species is still little explored. In this sense, the isolation and genomic characterization of new Lb. plantarum of Brazilian biodiversity could allow the discovery of exclusive protective mechanisms and presents potential for the development of alternative therapies to combat inflammation. As a result, a growing line of research, probiogenomics, has provided a more comprehensive and assertive understanding of the molecular bases of these probiotics. In this context, through the application of bioinformatics analyses, this work aimed to taxonomically and functionally characterize the complete genomes of six strains isolated in Brazil. In this way, the taxonomy of the six lineages was confirmed using the Average Nucleotide Identity by BLAST (ANIb), using the genome of the Lb lineage as a reference. plantarum SK151 from the GENBANK database (NCBI). In contrast, a multilocus phylogenetic analysis was performed using 220 complete Lb genomes. plantarum from the aforementioned database, to investigate evolutionary relationships with other probiotic lineages of the same species. Our results suggest high genetic proximity to probiotics already marketed, or that have demonstrated anti-inflammatory effects in clinical trials or preclinical studies of inflammatory diseases. Next, the analysis of antimicrobial peptides in the genomes of Brazilian isolates identified several plantaricin genes, suggesting antimicrobial potential. The presence of the gadB gene was also identified in the six lineages, which may be involved in the production of gamma-aminobutyric acid through the action of the enzyme glutamate decarboxylase, suggesting an important role in the regulation of the intestine-brain axis. Through SNP analyzes and molecular modeling, the lpl4 lineage showed a high degree of genetic and structural conservation of this enzyme when compared to the homologous protein considered functional in the Taj-Apis362 lineage. Furthermore, pangenomic analysis among all strains revealed the presence of exclusive genes in the lpl4 strain, namely, five hypothetical proteins and a sulfotransferase, involved in the synthesis of vitamin B6. To analyze the safety of the strains, the presence of antibiotic resistance genes was investigated, where only one marker was observed in a region of genomic plasticity on the chromosome of the E6 strain. Therefore, it is possible to conclude that the strains evaluated have probiotic properties with therapeutic potential for inflammatory diseases that affect the intestine-brain axis, especially lpl4, and can be considered safe for human and animal use. However, more studies are needed to investigate its therapeutic potential.

Foodborne Diseases are public health events with immediate compulsory notification and often associated with the consumption of animal products contaminated by bacteria. Escherichia coli is the main pathogen involved in foodborne outbreaks in Brazil. In recent years, free-range poultry products have shown greater visibility in the market. However, may there is negligence in terms of health surveillance for the marketing of these products, which provides health risk due to the greater possibility of spreading pathogenic microorganisms, including those resistant to antimicrobials. The aim was to investigate the presence of Escherichia coli in free-range poultry products sold informally and evaluate antimicrobials resistant E. coli circulation. Therefore, 38 free-range egg pools and 26 free-range chicken carcasses from informal marketing in Salvador-Bahia were analyzed. 30 isolates were obtained and identified as Escherichia coli by MALDI-TOF, with contamination rate of 92.3% (24/26 carcasses) of meat samples and 15.8% (6/38 pools) of egg samples. The isolates were submitted to the VITEK®2 System to determine the susceptibility pattern to clinically relevant classes of antimicrobials, such as penicillins, cephalosporins and carbapenems of the β-lactam group, aminoglycosides and quinolones. A total index of 46.7% (14/30) of resistance to at least one of tested antimicrobials was identified, with 35.7% (5/14) characterized as multidrug-resistants because they presented resistance to three or more classes of antimicrobials. The prevalence of resistance was higher for Ciprofloxacin with 33.3% (10/30), Ceftriaxone with 26.7% (8/30) and Ampicillin /Sulbactam with 20% (6/30). 8/30 (26.7%) presented phenotype for Extended-Spectrum Beta-Lactamase (ESBL) producing. In molecular characterization by PCR, 60% (18/30) of E. coli isolates were characterized as DEC group, with a higher prevalence for the atypical EAEC [38.9% (7/18)] and DAEC [22, 0% (4/18)], in addition to characterization of hybrid strains. Of the 30 isolates, 19 (63.3%) presented at least one β-lactam resistance gene, with a higher frequency observed for the blaCTX-M 1 and blaTEM genes, with 63% (12/19) and 47% (9/19), respectively, followed by blaOXA-1 and blaSHV with 10.5% (2/19) each. The detection of diarrheagenic, multidrug-resistant and/or ESBL-producing E.coli in free-range poultry products sold in a country for tourist purposes confirms the potential for these microorganisms to be transmitted through production animals, hence contributing to the occurrence of Foodborne Diseases and the global emergence of antimicrobial resistance.

Equine Infectious Anemia is caused by a Lentivirus that affects equids all over the world and clinical manifestation ranges from an asymptomatic to a lethal disease. There is no reliable vaccine, so the disease control and management, as recommended by the sanitary authorities includes testing animals before relocation and euthanasia for the positive ones. Due to the gravity of the disease and the fact that the diagnosis settles the destiny of animals’ lives, it is crucial that diagnostic be the most accurate as possible. The golden standard diagnosis method is Agarose Gel Immunodiffusion (AGID) with virion core protein p26, obtained from eukaryotic cell culture, as antigen. As the technology has improved, it is possible to produce viral proteins using the recombinant DNA and use them as antigen to develop more effective tests. The precursor protein Pr55gag shares antigenicity with the structural proteins of EIAV into which it is cleaved, therefore it should promote greater sensitivity to the diagnostic test. This study aimed to produce the Pr55gag protein in a prokaryotic system to avaluate its potential as an antigen in serological diagnosis. Thus, EIAV gag gene was inserted in plasmid pET_TEV that was cloned into Escherichia coli C41 (DE3) linage. This expression system was used to express the protein inducted with IPTG. The protein was purified on a histidine affinity column, underwent dialysis in PBS to remove excess salts and imidazole and was concentrated with a VivaSpin® system of centrifugation. The recombinant protein obtained from this methodology was used as an antigen in a Western blotting, in which 56 equine sera provided by the State Agricultural Defense Agency of Bahia (ADAB) and previously submitted to AGID were tested. Kappa coefficient of 0.82 indicates an almost perfect agreement between the results of both tests. In addition to being faster to perform, it is suggested that Western blotting with the recombinant protein is more sensitive, as it was able to identify more positive animals (23/56) than IDGA (19/56). Preliminary results suggest that the recombinant protein Pr55gag, obtained quickly, efficiently, with low cost and satisfactory yield, can be used as an antigen in diagnostic tests for Equine Infectious Anemia providing a more sensitive test by detecting a higher number of positive animals.

One of the decade’s most important discoveries in biotechnology is a defense mechanism found in prokaryotes that concedes adaptative immunity to its owner. This system called CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) consists in genomic integration of some sequences from bacteriophages, creating cellular “memory”. At this point, there are few studies about CRISPR’s role in prokaryotes’ interactions with the environment and organisms other than viruses. There is also little knowledge about how bacteria acquire this mechanism and its prevalence in species of economical interest, like phytopathogens. With this work, we intend to identify and classify CRISPR sequences found in the Xanthomonas genus, describing how this system affects interactions between the bacteria, their host plants and environmental viruses. In addition, we verify the hypothesis concerning these sequences’ origins in each Xanthomonas species, considering environmental influences and inheritance from a common ancestor. 239 complete Xanthomonas genomes were analyzed and CRISPR sequences were found in 102 of them. The final results imply that both environmental conditions and the common ancestor play a part to determine the presence, absence and characterization of CRISPR sequences in Xanthomonas. Therefore, it’s possible that both hypotheses are partially correct. Vast diversity observed in the spacers across the genomes indicates an intense network of environmental interactions to which bacteria are subordinated in order to carry out their phytopathogenic role.

Aquatic hyphomycete fungi are primary responsible for the process of decomposition in the allochthonous organic matter in headwater streams. Black waters streams have low leaf decomposition rate, fungal biomass and reproductive diversity of aquatic hyphomycetes. We hypothesize that the rates of fungal decomposition and colonization are low due to the low concentration of nutrients, acid pH and higher concentration of humic acid in these streams. In a microcosms conditions we tested a complete factorial design (3 [humic acid levels: 5 and 24mgL^-1] x 2 [nutrient levels: 0.05mgL^-1 nitrogen and 0.07mgL^-1 phosphorus and 0.5mgL^{- 1} of nitrogen and 0.7 mgL^-1 of phosphorus x 2 [two pH ranges: 4 and 7.8] + 3 [controls: river water] x 3 replicates). Senescent leaves of Miconia albicans were incubated in fine mesh bags for 15 days in 3 clear water streams for colonization by aquatic hyphomycetes. In the laboratory, a set of 10 discs from the pre-colonized leaves, for each incubation stream, was distributed in each treatment. Every three days the nutrient solution containing the suspension spores was changed and preserved in formalin (4%) to determine the richness, density and reproduction rate of the aquatic hyphomycetes. We identified 15 species of aquatic hyphomycetes associated with leaf litter in breakdown process. Flagelospora curvula, Lunullopora curvula and Triscelophorus monosporus were the most abundance organism in conidia production. Nitrogen was the main factor that drive fungal biomass, fungal sporulation density and richness, but not leaf litter breakdown. Statistical models suggest that higher concentrations of humic acid, low nitrogen availability and acidic pH negatively affect the leaf decomposition process and alter the aquatic hyphomycete community. Although, our study was carried out in vitro, new hypotheses about the decomposition process in black waters of tropical Brazilian savannah may note future investigations in this unique ecosystem, mainly to understand the interactions between humic substances and aquatic hyphomycetes.

Bacteria of the genus Leptospira comprehend 66 genomic species including pathogenic, intermediate and saprophytic groups. Pathogenic leptospires are the etiologic agent of leptospirosis, a disease of public health impact worldwide. Biofilms improve survival of microorganisms in hostile environments and are related to various medical conditions. Leptospira forms biofilms in vitro and in vivo. Nevertheless, the regulatory mechanisms of biofilm formation in Leptospira are poorly known. We aimed in this study to identify transcriptional regulators involved in biofilm formation in Leptospira biflexa and describe the co-regulation networks of these regulators. First, we collected transcriptional regulators predicted for Leptospira biflexa in the P2TF database. Than, a similarity search was conducted using BLASTp of those regulators against previous data from a Leptospira biflexa transcriptome analysis of biofilm versus planktonic cells, in two time points: 48h (mature) and 120 h (late). After identifying regulatory genes in Leptospira biflexa, we checked for their expression levels. We found 138 transcriptional regulators predicted for this species, comprising sigma factors, one-component systems, response regulators and other DNA-binding proteins. From those, 38 presented were identified  as participating in biofilm regulation. Leptospira genomes are poorly known, with half of it composed of hypothetical proteins. We believe our results will pave the way for an initial comprehension of the regulatory mechanisms in Leptospira biofilm.

Aquatic hyphomycetes (AH) are decomposer fungus of submersed organic matter. The objective of this work was to evaluate whether black waters affect the reproduction and activity of AH. For this matter, we executed two experiments. Experiment 1: leaves of Miconia albicans and Davilla angustifólia (Atlantic Forest); Clusia burlemaxxi and Vochysia acuminata (Brazilian savanna) were incubated in a low order stream of their respective biomes (the Brazilian savanna stream representing black waters and the Atlantic forest stream representing white waters). We did not find a significative difference in the decomposition rates between the black waters and white waters streams; however, sporulation rate and fungal biomass were higher in the white waters streams. Experiment 2: leaves of M. albicans e C. burlemaxxi were incubated in streams of their respective biomes, and after 15 days of incubation, half of the experiment was transplanted between the streams (litter bags from white waters streams were placed into black waters streams and vice versa). After the transplant the decomposition rates were slightly accelerated, but there was no significative difference between treatments (RM-ANOVA p>0,05). Twenty-one (21) AH species were identified associated to decomposing leaves. No structural change in the AH community was detected after the streams transplant. The sporulation rate and the fungal biomass were higher in the white waters streams. Therefore, we assume that black waters are unfavorable for the reproductive activity of AH.

Biofilms are the main way of life of microorganisms in nature. In this phenotype, bacteria
have unique metabolic characteristics, including changes in growth such as cell size and
generation time. Leptospires, whose pathogenic species cause leptospirosis, form biofilms
in vitro and in natural environments. There is little information on the metabolism of
leptospires in biofilms. In this work we analyzed physiological and genomic aspects of
Leptospira growth in biofilms. We cultivated the saprophytic species Leptospira biflexa in
biofilms (BIOF) and planktonic cells (PLANK) for seven days at 29ºC. We performed
growth curves by counting bacteria every 12 h. For the cell viability test, we stained the
biofilms with the Live / Dead reagent, with observation under a fluorescence microscope.
We measured the cell length for morphological evaluation during the growth phases. We
analyzed the differential expression of OmpL36 structural protein by Western blotting,
comparing BIOF and PLANK. Finally, we performed analysis of growth gene homologies
in the complete genome of L. biflexa and of the transcriptional expression of the identified
genes (Bioproject PRJNA288909). BIOF and PLANK cells presented classic growth curves.
The mean generation time (GT) was 4.9 h (± 0.32) for BIOF, two hours less than for PLANK
(6.9 h ± 0.24). Despite the faster growth demonstrated by lower GT, the cell concentration
of BIOF was approximately ten times lower than that of PLANK. The viability test showed
that leptospires in the biofilm began to die earlier, with 24 h of incubation, during
exponential phase, which may explain the lower concentration of cells observed for this
phenotype. In addition, we observed negative regulation of 58% of growth genes in the
biofilm. This change was more prominent in mature biofilm (48 h) when cells are in
transition to stationary state. Cell length analyzes showed longer BIOF cells during
stationary and decline phases. The OmpL36 protein was more expressed in the mature
biofilm than in planktonic cells. Collectively, our data provide evidence of metabolic
changes and growth limitation of Leptospira in biofilms.

Lignin is a three-dimensional amorphous macromolecule formed by binding, predominating
β-aryl ether between coumaril, synapyl and coniferyl alcohols. Justified by the recalcitrance
of lignin, the search for naturally biodegrading bacteria lignin has been the subject of studies
because they are easy to grow and manipulate, but it does not have a complete understanding
of how bacteria have the ability to degrade lignin. Aiming to identify and characterize the
lignin degradation system of environmental prokaryotes, we used dependent and
independent approaches to culture. In order to achieve this, in chapter 1, culture-dependent
approaches allowed taxonomic identification and functional characterization of lineages of
bacteria FP10-5.22 (Klebsiella variicola), P3TM1 (Klebsiella variicola) and FP10-5.23
(Klebsiella oxytoca), which presented growth capacity in lignin as the sole carbon source
(stationary phase in 24 hours) and up to 98% degradation of the methylene blue dye in 48
hours. In chapter 2, the data referring to the sequencing of the complete genome of the
ligninolytic line P1CD1 (K. variicola) are presented. The sequencing of the complete
genome allowed the identification of the genetic repertoire involved in the degradation of
lignin, as well as to establish the possible metabolic routes used by the lineage P1CD1 to
degrade lignin. 251 genes related to transferase, dehydrogenase, lyase,
transcriptional/regulatory, monooxygenase, dioxygenase, reductase, hydrolase, peroxidase,
isomerase, oxidase, transport, ligase, hydroxylase, superoxide and redox proteins have been
identified. The identified genetic repertoire suggests that lignin is degraded in two steps; the
first step relates to the depolymerization of the primary lignin molecule (decoupling of the
precursor alcohols interunit bonds) by the activity of the lignin-modifying enzymes (LMEs)
and the auxiliary of lignin degradation enzymes of (LDAs) generating peripheral
metabolites. The second stage is related to the decomposition of lignin-derived fragments
through the activity of the enzymes present in the subsystems belonging to the metabolism
of aromatic compounds, transforming the peripheral metabolites into intermediary lignin
metabolites. The results of chapters 1 and 2 suggest that prokaryotes of Caatinga water and
soil samples are a viable alternative for the optimization of the pre-treatment stage of
lignocellulosic biomass, since they presented high ligninolytic potential after genomic and
phenotypic analysis.