From the Andes to the desert: First overview of the bacterial community in the Rimac river, the main source of water for Lima, Peru

AbstractBackgroundThe Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. We aim to produce the first characterization of bacterial communities in the Rimac river using a 16S rRNA amplicon sequencing approach which would be useful to identify bacterial diversity and potential understudied pathogens.ResultsWe report a higher diversity in bacterial communities from the Upper and, especially, Middle Rimac compared to the Lower Rimac (Metropolitan zone). Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility, quorum sensing and xenobiotics metabolism. Additional metabolomic analyses showed the presence natural flavonoids and antibiotics in the Upper Rimac, and herbicides in the Lower Rimac.ConclusionsThe dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, but that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

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From the Andes to the desert: 16S rRNA metabarcoding characterization of aquatic bacterial communities in the Rimac river, the main source of water for Lima, Peru

PLoS ONE ◽

10.1371/journal.pone.0250401 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0250401

Author(s):

Pedro E. Romero ◽

Erika Calla-Quispe ◽

Camila Castillo-Vilcahuaman ◽

Mateo Yokoo ◽

Hammerly Lino Fuentes-Rivera ◽

...

Keyword(s):

16S Rrna ◽

Metropolitan Area ◽

Bacterial Communities ◽

Geographical Location ◽

Microbiological Quality ◽

Urban Sewage ◽

The Andes ◽

Metabolic Functions ◽

Quality Assessments

The Rimac river is the main source of water for Lima, Peru’s capital megacity. The river is constantly affected by different types of contamination including mine tailings in the Andes and urban sewage in the metropolitan area. In this work, we aim to produce the first characterization of aquatic bacterial communities in the Rimac river using a 16S rRNA metabarcoding approach which would be useful to identify bacterial diversity and potential understudied pathogens. We report a lower diversity in bacterial communities from the Lower Rimac (Metropolitan zone) in comparison to other sub-basins. Samples were generally grouped according to their geographical location. Bacterial classes Alphaproteobacteria, Bacteroidia, Campylobacteria, Fusobacteriia, and Gammaproteobacteria were the most frequent along the river. Arcobacter cryaerophilus (Campylobacteria) was the most frequent species in the Lower Rimac while Flavobacterium succinicans (Bacteroidia) and Hypnocyclicus (Fusobacteriia) were the most predominant in the Upper Rimac. Predicted metabolic functions in the microbiota include bacterial motility and quorum sensing. Additional metabolomic analyses showed the presence of some insecticides and herbicides in the Parac-Upper Rimac and Santa Eulalia-Parac sub-basins. The dominance in the Metropolitan area of Arcobacter cryaerophilus, an emergent pathogen associated with fecal contamination and antibiotic multiresistance, that is not usually reported in traditional microbiological quality assessments, highlights the necessity to apply next-generation sequencing tools to improve pathogen surveillance. We believe that our study will encourage the integration of omics sciences in Peru and its application on current environmental and public health issues.

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Intergenerational microbial transmission in the little skate (Leucoraja erinacea)

10.1101/2020.12.30.424594 ◽

2020 ◽

Author(s):

Katelyn Mika ◽

Alexander S. Okamoto ◽

Neil H. Shubin ◽

David B. Mark Welch

Keyword(s):

Bacterial Communities ◽

Internal Surface ◽

Amplicon Sequencing ◽

Site Specific ◽

Bacterial Phyla ◽

16S Rrna Amplicon Sequencing ◽

Primary Mechanism ◽

Bacterial Transmission ◽

Embryonic Skin ◽

Egg Capsule

AbstractMicrobial transmission from parent to offspring is hypothesized to be universal in vertebrates. However, evidence for this is limited as many clades remain unexamined. Chondrichthyes, as one of the earliest–branching vertebrate lineages, provide an opportunity to investigate the phylogenetic breadth of this hypothesis. To assess the potential for bacterial transmission in an oviparous chondrichthyan, we used 16S rRNA amplicon sequencing to characterize the microbial communities associated with the skin, gill, and egg capsule of the little skate, Leucoraja erinacea, at six points during ontogeny. We identify site-specific microbiomes dominated by the bacterial phyla Proteobacteria and Bacteroidetes, a composition similar to, but distinct from, that of other chondrichthyans. Our data reveal that the skate egg capsule harbors a highly diverse bacterial community–particularly on the internal surface of the capsule–and facilitates intergenerational microbial transfer to the offspring. Embryonic skin and external gill tissues host similar bacterial communities; the skin and gill communities later diverge as the internal gills and skin denticles develop. Our study is the first exploration of the chondrichthyan microbiome throughout ontogeny and provides the first evidence of vertical transmission in this group, which may be the primary mechanism for the signature of phylosymbiosis previously observed in elasmobranchs.

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Localization of bacterial communities within gut compartments across Cephalotes turtle ants

Applied and Environmental Microbiology ◽

10.1128/aem.02803-20 ◽

2021 ◽

Author(s):

Peter J. Flynn ◽

Catherine L. D’Amelio ◽

Jon G. Sanders ◽

Jacob A. Russell ◽

Corrie S. Moreau

Keyword(s):

Microbial Community ◽

Microbial Communities ◽

Digestive Tract ◽

Bacterial Communities ◽

Evolutionary History ◽

Amplicon Sequencing ◽

Caste Differentiation ◽

Animal Group ◽

16S Rrna Amplicon Sequencing ◽

Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

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Indoor-Biofilter Growth and Exposure to Airborne Chemicals Drive Similar Changes in Plant Root Bacterial Communities

Applied and Environmental Microbiology ◽

10.1128/aem.00595-14 ◽

2014 ◽

Vol 80 (16) ◽

pp. 4805-4813 ◽

Cited By ~ 13

Author(s):

Jacob A. Russell ◽

Yi Hu ◽

Linh Chau ◽

Margarita Pauliushchyk ◽

Ioannis Anastopoulos ◽

...

Keyword(s):

Indoor Air ◽

Bacterial Communities ◽

Plant Root ◽

Amplicon Sequencing ◽

Biomass Energy ◽

Plant Roots ◽

Content Type ◽

16S Rrna Amplicon Sequencing ◽

Wide Range ◽

Different Strains

ABSTRACTDue to the long durations spent inside by many humans, indoor air quality has become a growing concern. Biofiltration has emerged as a potential mechanism to clean indoor air of harmful volatile organic compounds (VOCs), which are typically found at concentrations higher indoors than outdoors. Root-associated microbes are thought to drive the functioning of plant-based biofilters, or biowalls, converting VOCs into biomass, energy, and carbon dioxide, but little is known about the root microbial communities of such artificially grown plants, how or whether they differ from those of plants grown in soil, and whether any changes in composition are driven by VOCs. In this study, we investigated how bacterial communities on biofilter plant roots change over time and in response to VOC exposure. Through 16S rRNA amplicon sequencing, we compared root bacterial communities from soil-grown plants with those from two biowalls, while also comparing communities from roots exposed to clean versus VOC-laden air in a laboratory biofiltration system. The results showed differences in bacterial communities between soil-grown and biowall-grown plants and between bacterial communities from plant roots exposed to clean air and those from VOC-exposed plant roots. Both biowall-grown and VOC-exposed roots harbored enriched levels of bacteria from the genusHyphomicrobium. Given their known capacities to break down aromatic and halogenated compounds, we hypothesize that these bacteria are important VOC degraders. While different strains ofHyphomicrobiumproliferated in the two studied biowalls and our lab experiment, strains were shared across plant species, suggesting that a wide range of ornamental houseplants harbor similar microbes of potential use in living biofilters.

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Two Distinct Soil Disinfestations Differently Modify the Bacterial Communities in a Tomato Field

Agronomy ◽

10.3390/agronomy11071375 ◽

2021 ◽

Vol 11 (7) ◽

pp. 1375

Author(s):

Masaru Nakayasu ◽

Kyoko Ikeda ◽

Shinichi Yamazaki ◽

Yuichi Aoki ◽

Kazufumi Yazaki ◽

...

Keyword(s):

Environmental Factors ◽

Bacterial Communities ◽

Quantitative Polymerase Chain Reaction ◽

Amplicon Sequencing ◽

Growth And Yield ◽

16S Rrna Amplicon Sequencing ◽

Tomato Field ◽

Pathogen Suppression ◽

Polymerase Chain ◽

Soil Environmental Factors

Reductive soil disinfestation (RSD) and soil solarization (SS) were evaluated based on environmental factors, microbiome, and suppression of Fusarium oxysporum in a tomato field soil. Soil environmental factors (moisture content, electric conductivity, pH, and redox potential (RP)) were measured during soil disinfestations. All factors were more strongly influenced by RSD than SS. 16S rRNA amplicon sequencing of RSD- and SS-treated soils was performed. The bacterial communities were taxonomically and functionally distinct depending on treatment methods and periods and significantly correlated with pH and RP. Fifty-four pathways predicted by PICRUSt2 (third level in MetaCyc hierarchy) were significantly different between RSD and SS. Quantitative polymerase chain reaction demonstrated that both treatments equally suppressed F. oxysporum. The growth and yield of tomato cultivated after treatments were similar between RSD and SS. RSD and SS shaped different soil bacterial communities, although the effects on pathogen suppression and tomato plant growth were comparable between treatments. The existence of pathogen-suppressive microbes, other than Clostridia previously reported to have an effect, was suggested. Comparison between RSD and SS provides new aspects of unknown disinfestation patterns and the usefulness of SS as an alternative to RSD.

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Characterization and comparison of the bacterial communities of rhizosphere and bulk soils from cadmium-polluted wheat fields

PeerJ ◽

10.7717/peerj.10302 ◽

2020 ◽

Vol 8 ◽

pp. e10302

Author(s):

Li Song ◽

Zhenzhi Pan ◽

Yi Dai ◽

Lin Chen ◽

Li Zhang ◽

...

Keyword(s):

Bacterial Community ◽

Contaminated Soils ◽

Bacterial Communities ◽

Cadmium Concentration ◽

Normal Growth ◽

Amplicon Sequencing ◽

Negative Influence ◽

Cadmium Pollution ◽

16S Rrna Amplicon Sequencing ◽

The Impact

Cadmium pollution is becoming a serious problem due to its nondegradability and substantial negative influence on the normal growth of crops, thereby harming human health through the food chain. Rhizospheric bacteria play important roles in crop tolerance. However, there is little experimental evidence which demonstrates how various cadmium concentrations affect the bacterial community in wheat fields including rhizosphere microorganisms and nonrhizosphere (bulk) microorganisms. In this study, 16S rRNA amplicon sequencing technology was used to investigate bacterial communities in rhizosphere and bulk soils under different levels of pollution in terms of cadmium concentration. Both the richness and diversity of the rhizosphere microorganism community were higher under nonpolluted soil and very mild and mild cadmium-contaminated soils than compared with bulk soil, with a shift in community profile observed under severe cadmium pollution. Moreover, cadmium at various concentrations had greater influence on bacterial composition than for the nonpolluted site. In addition, redundancy analysis (RDA) and Spearman’s analysis elucidated the impact of exchangeable Cd and total Cd on bacterial community abundance and composition. This study suggests that cadmium imposes a distinct effect on bacterial community, both in bulk and rhizosphere soils of wheat fields. This study increases our understanding of how bacterial communities in wheat fields shaped under different concentrations of cadmium.

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Land Use Effects on Airborne Bacterial Communities Are Evident in Both Near-Surface and Higher-Altitude Air

Diversity ◽

10.3390/d13020085 ◽

2021 ◽

Vol 13 (2) ◽

pp. 85

Author(s):

Allison M. Spring ◽

Kenneth D. Domingue ◽

Thomas V. Kerber ◽

Margaret M. Mooney ◽

Rebecca L. Hale ◽

...

Keyword(s):

Land Use ◽

Bacterial Communities ◽

Amplicon Sequencing ◽

Small Scale ◽

Dispersal Patterns ◽

Near Surface ◽

Operational Taxonomic Units ◽

16S Rrna Amplicon Sequencing ◽

Surface Samples ◽

Land Use Effects

Land use influences the composition of near-surface airborne bacterial communities, and bacteria can be transported through the atmosphere at global scales. The atmosphere mixes vertically, but rigorously assessing whether the effects of land use on atmospheric communities extends to higher altitudes requires examining communities from multiple altitudes collected at a stable location and timeframe. In this study, we collected near-surface (<2 m) and higher-altitude (150 m) air samples from three sites in an agricultural/developed location and a forested/undeveloped location. We used bacterial 16S rRNA amplicon sequencing to compare communities and predict functionality by altitude. Higher-altitude and near-surface communities did not differ in composition within each location. Communities collected above the undeveloped location were equally variable at both altitudes; higher-altitude samples from the developed location predominantly contained Firmicutes and were less variable than near-surface samples. We also compared airborne taxa to those present in soil and snow. Communities from higher-altitude samples above the developed location contained fewer overlapping taxa with soil and snow sources, and overlapping Operational Taxonomic Units (OTUs) among the three sources differed by location. Our results suggest that land use affects the composition of both near-surface and higher-altitude airborne bacterial communities and, therefore, may influence broad bacterial dispersal patterns. This small-scale pilot study provides a framework for simultaneously examining local and regional airborne microbial communities that can be applied to larger studies or studies using different types of samplers.

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Analysis of Bacterial Diversity in Relation to the Presence of the Top 7 Shiga Toxin–Producing Escherichia coli throughout Australian Beef Abattoirs

Journal of Food Protection ◽

10.4315/jfp-20-109 ◽

2020 ◽

Vol 83 (10) ◽

pp. 1812-1821

Author(s):

SANGA KANG ◽

JOSHUA T. RAVENSDALE ◽

RANIL COOREY ◽

GARY A. DYKES ◽

ROBERT S. BARLOW

Keyword(s):

Escherichia Coli ◽

Bacterial Diversity ◽

Shiga Toxin ◽

Bacterial Communities ◽

Alpha Diversity ◽

Amplicon Sequencing ◽

Bacterial Composition ◽

16S Rrna Amplicon Sequencing ◽

Surface Samples ◽

Inspection Service

ABSTRACT There is increasing evidence that diversity changes in bacterial communities of beef cattle correlate to the presence of Shiga toxin–producing Escherichia coli (STEC). However, studies that found an association between STEC and bacterial diversity have been focused on preslaughter stages in the beef supply chain. This study was designed to test a hypothesis that there are no differences in bacterial diversity between samples with and those without the presence of the top 7 STEC (O26, O45, O103, O111, O121, O145, and O157) throughout processing in an integrated (abattoir A) and a fragmented (abattoir B) Australian beef abattoir. Slaughter and boning room surface samples from each abattoir were analyzed using 16S rRNA amplicon sequencing and tested for the top 7 STEC following the Food Safety and Inspection Service protocol. Potential positives through slaughter were similar between the abattoirs (64 to 81%). However, abattoir B had substantially reduced potential positives in the boning room compared with abattoir A (abattoir A: 23 and 48%; abattoir B: 2 and 7%). Alpha diversity between the sample groups was not significantly different (P > 0.05) regardless of different STEC markers. Nonmetric multidimensional scaling of slaughter samples showed that the bacterial composition in fecal and hide samples shared the least similarity with the communities in carcass and environmental samples. Surface samples from slaughter (carcass and environmental) and boning (carcass, beef trim, and environmental) all appeared randomly plotted on the scale. This indicated that the STEC presence also did not have a significant effect (P > 0.05) on beta diversity. Although presence of STEC appeared to correlate with changes in diversity of fecal and hide bacterial communities in previous studies, it did not appear to have the same effect on other samples throughout processing. HIGHLIGHTS

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Composition and Potential Functions of Rhizobacterial Communities in a Pioneer Plant from Andean Altiplano

Diversity ◽

10.3390/d14010014 ◽

2021 ◽

Vol 14 (1) ◽

pp. 14

Author(s):

Qian Zhang ◽

Macarena M. Araya ◽

Marcia Astorga-Eló ◽

Gabriela Velasquez ◽

Joaquin I. Rilling ◽

...

Keyword(s):

Atacama Desert ◽

Amplicon Sequencing ◽

Potential Functions ◽

Solar Irradiation ◽

16S Rrna Amplicon Sequencing ◽

The Andes ◽

Pioneer Plants ◽

Pioneer Plant ◽

Andean Altiplano ◽

Harsh Conditions

Plant microbiota that associate with pioneer plants are essential to their growth and adaptation to harsh conditions found in the Central Volcanic Zone of the Andes. In this sense, the rhizosphere of pioneer species represents a unique opportunity to examine how bacterial communities are recruited and support the growth of plants under abiotic stress conditions, such low nutrient availability, high solar irradiation, water scarcity, soil salinity, etc. In this study, we explored the community composition and potential functions of rhizobacteria obtained from specimens of Parastrephia quadrangularis (Meyen) Cabrera, commonly called Tola, grown on the slopes of the Guallatiri, Isluga, and Lascar volcanoes in the Atacama Desert of Chile by using 16S rRNA amplicon sequencing. Sequence analysis showed that the Actinobacteria, Proteobacteria, Acidobacteria, and Bacteroidetes were the most abundant phyla of the rhizobacterial communities examined. A similar diversity, richness, and abundance of OTUs were also observed in rhizosphere samples obtained from different plants. However, most of OTUs were not shared, suggesting that each plant recruits a specific rhizobacterial communities independently of volcanoes slope. Analyses of predicted functional activity indicated that the functions were mostly attributed to chemoheterotrophy and aerobic chemoheterotrophy, followed by nitrogen cycling (nitrate reduction and denitrification), and animal parasites or symbionts. In addition, co-occurrence analysis revealed that complex rhizobacterial interactions occur in P. quadrangularis rhizosphere and that members of the Patulibacteraceae comprise a keystone taxon. This study extends our understanding on the composition and functions of the rhizobiome, which is pivotal for the adaptability and colonization of pioneer plant to harsh conditions of the Atacama Desert, widely recognized as the driest place on planet Earth.

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