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ABSTRACT We provide a collection of 78 bacterial isolates from the rhizosphere of switchgrass ( Panicum virgatum L .) at the Lux Arbor Reserve in Delton, MI, a site of the Great Lakes Bioenergy Research Center (GLBRC), Michigan State University, MI, USA. We include information on isolation conditions and full-length 16S rRNA sequences.
The light-harvesting 2 (LH2) complex of purple phototrophic bacteria plays a critical role in absorbing solar energy and distributing the excitation energy. Exciton dynamics within LH2 complexes are controlled by the structural arrangement and energy levels of the bacteriochlorophyll (BChl) and carotenoid (Car) pigments. However, there is still debate over the competing light-harvesting versus energy-dissipation pathways. In this work, we compared five variants of the LH2 complex from genetically modified strains of Rhodobacter sphaeroides, all containing the same BChls but different Cars with increasing conjugation: zeta-carotene (N = 7; LH2 Zeta ), neurosporene (N = 9; LH2 Neu ), spheroidene (N = 10; LH2 Spher ), lycopene (N = 11; LH2 Lyco ), and spirilloxanthin (N = 13; LH2 Spir ). Absorption measurements confirmed that the Car excited-state energy decreased with increasing conjugation. Similarly, fluorescence spectra showed that the B850 BChl emission peak had an increasing red shift from LH2 Zeta →(LH2 Neu /LH2 Spher )→LH2 Lyco →LH2 Spir . In contrast, time-resolved fluorescence and ultrafast transient absorption (fs-TA) revealed similar excited-state lifetimes (∼1 ns) for all complexes except LH2 Spir (∼0.7 ns). From fs-TA analysis, an additional ∼7 ps nonradiative dissipation step from B850 BChl was observed for LH2 Zeta . Further, singlet− singlet and singlet−triplet annihilation studies showed a ∼50% average fluorescence lifetime reduction in LH2Zeta at high laser power and high repetition rate, compared to ∼10−15% reductions in LH2 Neu /LH2 Spher /LH2 Lyco and minimal lifetime change in LH2 Spir . In LH2 Zeta , the fastest decay component (<50 ps) became prominent at high repetition rates, consistent with strong singlet−triplet annihilation. Nanosecond TA measurements revealed long-lived (>40 μs) BChl triplet states in LH2 Zeta and signs of damage caused by singlet oxygen, whereas other LH2s showed faster triplet quenching (∼18 ns) by Cars. These findings highlight a key design principle of LH2 complexes: the Car triplet energy must be significantly lower than the BChl triplet energy to efficiently quench BChl triplets that otherwise act as potent “trap states,” causing exciton annihilation in laser-based experiments or photodamage in native membranes.
We report the draft genomes of a collection of 15 bacteria, isolated from the rhizosphere soil of bioenergy sorghum (Sorghum bicolor (L.) Moench). These isolates belong to the genera, Acidovorax, Nocardioides, Agrobacterium, Peribacillus, Caulobacter, Cupriavidus, Pseudomonas, Rhizobium, Sphingomonas, Priestia, Dyadobacter, Roseomonas, Ideonella, and Bacillus.
ABSTRACT Tattooing and use of permanent makeup (PMU) have dramatically increased over the last decade, with a concomitant increase in ink-related infections. Studies have shown evidence that commercial tattoo and PMU inks are frequently contaminated with pathogenic microorganisms. Considering that tattoo inks are placed into the dermal layer of the skin where anaerobic bacteria can thrive and cause infections in low-oxygen environments, the prevalence of anaerobic and aerobic bacteria should be assessed in tattoo and PMU inks. In this study, we tested 75 tattoo and PMU inks using the analytical methods described in the FDA Bacteriological Analytical Manual Chapter 23 for the detection of both aerobic and anaerobic bacterial contamination, followed by 16S rRNA gene sequencing for microbial identification. Of 75 ink samples, we found 26 contaminated samples with 34 bacterial isolates taxonomically classified into 14 genera and 22 species. Among the 34 bacterial isolates, 19 were identified as possibly pathogenic bacterial strains. Two species, namelyCutibacterium acnes(four strains) andStaphylococcus epidermidis(two strains) were isolated under anaerobic conditions. Two possibly pathogenic bacterial strains,Staphylococcus saprophyticusandC. acnes, were isolated together from the same ink samples (n= 2), indicating that tattoo and PMU inks can contain both aerobic (S. saprophyticus) and anaerobic bacteria (C. acnes). No significant association was found between sterility claims on the ink label and the absence of bacterial contamination. The results indicate that tattoo and PMU inks can also contain anaerobic bacteria. IMPORTANCE The rising popularity of tattooing and permanent makeup (PMU) has led to increased reports of ink-related infections. This study is the first to investigate the presence of both aerobic and anaerobic bacteria in commercial tattoo and PMU inks under aerobic and anaerobic conditions. Our findings reveal that unopened and sealed tattoo inks can harbor anaerobic bacteria, known to thrive in low-oxygen environments, such as the dermal layer of the skin, alongside aerobic bacteria. This suggests that contaminated tattoo inks could be a source of infection from both types of bacteria. The results emphasize the importance of monitoring these products for both aerobic and anaerobic bacteria, including possibly pathogenic microorganisms.
In diverse environments, microbes drive a myriad of processes, from geochemical and nutrient cycling to interspecies interactions, including associations with plants and animals. Their physiological state is dynamic and impacted by abiotic and biotic conditions, responding to environmental fluctuations by changes in cellular metabolism, according to their genetic potential. Molecular, cellular, and genomic approaches can identify and measure microbial responses and adaptation to environmental changes in native communities. However, isolating individual microbial cells that respond to specific changes for cultivation has been difficult. To address this, we implemented a novel bacterial isolation approach (BONCAT-Live) by integrating bio-orthogonal non-canonical amino acid tagging (BONCAT) in diverse native communities, with isolation and cultivation of cells responding to specific stimuli, at different time scales. In frozen Arctic permafrost samples, we identified and isolated dormant bacteria that become active after thawing under native or nutrient-enriched conditions. From the Populus tree rhizosphere, we isolated strains that thrive under high concentrations of root exudates that act as defense compounds and nutrients. In the human microbiome, we identified and isolated bacteria that rapidly proliferated when exposed to metabolites provided by the host or other co-occurring microbes. Further characterization of isolated bacterial strains will provide opportunities for in-depth determination of how these microbes adapt to changes in their environments, individually and as part of model communities.
Bacterial metabolic interactions with rare earth elements (REEs) can be harnessed for biomining unconventional feedstocks like abandoned coal-mine drainage (AMD). Pennsylvania has ~500 AMD passive remediation systems that can precipitate REE rich solids. REEs include yttrium and the lanthanide series that are used in modern energy and technology. Bacteria that metabolically interact with REEs can be used for biomining in an affordable efficient process that does not require hazardous chemical additives. Currently, the microbial metal mechanisms that contribute to REE biorelease and biorecovery are poorly understood. Our work shows acidogenic bacterial isolates (Bacillus mycoides JR07 and Bacillus pseudomycoides KB7) successfully bioleach a mixed REE solution from AMD solids by their organic acid production and biofilm formation. Further, our work shows the potential for bacterial lanthanide-dependent enzymes to recover lanthanides from a mixed REE solution; here we have bacterial isolate Methylobacterium sp. B3 that can recover soluble lanthanum. Whole genome sequencing of Methylobacterium sp. B3 predict lanthanide-dependent methanol dehydrogenase XoxF. Understanding the microbial metabolism and genes involved in the REE release and recovery is crucial to optimize the biomining of AMD solids. Our work addresses the growing need to develop novel REE mining methods from unconventional feedstocks.
This dataset contains binary carbon-source growth results for bacterial isolates associated with Populus roots. The isolates are part of the Populus culture collection described by Carper et al. (2021), Cultivating the Bacterial Microbiota of Populus Roots (https://doi.org/10.1128/msystems.01306-20).
Five bacterial isolates were isolated from the roots of poplar trees (Populus deltoides and P. trichocarpa), which are model organisms and a main focus of the Plant-Microbe Interfaces (PMI) project at ORNL. These strains belong to genera are not well represented and give a more complete view of the microbial community and bacterial interactions with poplar trees. These strains will support future studies and contribute to the broader PMI goal of understanding microbe-microbe and plant-microbe interactions.
Introduction Food spoilage and pathogenic bacteria on food-contact surfaces, especially biofilm-forming strains, can transfer to meats during processing. The objectives of this study were to survey the bacterial communities of beef cuts that transfer onto two commonly used food-contact surfaces, stainless steel (SS) and high-density polyethylene (HDPE) and identify potentially biofilm-forming strains. Methods Top round, flank, chuck, and ground beef were purchased from 3 retail stores. SS and HDPE coupons (approximately 2cm × 5cm) were placed on beef portions (3h, 10°C), after which, the coupons were submerged halfway in PBS (24h, 10°C). Bacteria from the beef cuts and coupon surfaces ( n = 3) were collected, plated on tryptic soy agar plates and incubated (5 days, 25°C). Bacterial isolates were identified by 16S rRNA gene amplicon sequencing and assayed for biofilm formation using a crystal violet binding (CV) assay (72h, 10°C). Additionally, beef and coupon samples were collected for bacterial community analysis by 16S rRNA gene amplicon sequencing. Results and discussion Sixty-one of 972 beef isolates, 29 of 204 HDPE isolates, and 30 of 211 SS isolates were strong biofilm-formers (Absorbance>1.000 at 590 nm in the CV assay). Strong-binding isolates identified were of the genera Pseudomonas , Acinetobacter , Psychrobacter , Carnobacterium , and Brochothrix . Coupon bacterial communities among stores and cuts were distinct ( p < 0.001, PERMANOVA), but there was no distinction between the communities found on HDPE or SS coupons ( p > 0.050, PERMANOVA). The bacterial communities identified on the coupons may help determine the communities capable of transferring and colonizing onto surfaces, which can subsequently cross-contaminate foods.
Abandoned Coal-Mine Drainage (AMD) is a source of critical minerals (CMs) that can be biomined to increase domestic CM production for the growing tech industry while mitigating current AMD hazardous waste. Pennsylvania has ~11,000 abandoned mines, ~500 of which are currently being treated with passive remediation systems (PRS), designed to increase the pH and precipitate AMD waste onsite. Manganese (Mn) that precipitates from AMD waste can co-precipitate with CMs, and the Mn and CMs will accumulate on the PRS solids over the treatment period. This results in high Mn/CM solids that could produce a valuable leachate if resolubilized. Mn reduction and solubilization can occur through microbial driven geochemical changes such as the acidification of the environment, and it is expected that Mn resolubilization will lead to a co-resolubilization of the CMs. Investigation and stimulation of this microbial resolubilization could result in an affordable CM release process that does not require chemical additives into the environment. However the microbial mechanisms that contribute to Mn resolubilization are poorly understood. Here, we have isolated bacteria capable of resolubilizing Mn from AMD PRS. Five of the bacteria isolates have been identified as Bacillus spp. and two as Corynebacterium spp. that ferment glucose to reduce/solubilize Mn MnO2 by acidogenesis. The bacterial isolates are also capable of solubilizing Mn and CMs (Y, Zr, Sb, La, Ce, Pr, Nd, Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu) from AMD PRS precipitated solids through their production of organic acids. Determining the microbial metabolism and genes involved in the resolubilization of manganese is crucial to optimize the biomining of CMs from AMD solid precipitants. This work addresses the growing need to develop novel CM recovery methods from domestic sources.
Microbes can be used for biomining rare earth elements (REEs) from abandoned coal-mine drainage (AMD) solids. Domestically Pennsylvania has ~11,000 abandoned mines, with ~500 AMD passive remediation systems (PRSs) that precipitate REE rich solids. In passive systems, REEs, co-precipitate with manganese (Mn), accumulating as a valuable leachate when resolubilized. REEs like lanthanum (La) are used in battery technology. Microbial metabolism that co-resolubilize Mn and REEs could result in an affordable release process that does not require the addition of hazardous chemical additives. Microbial sequestering of La can be used for selective purification from a mixed REE composition. Currently, the microbial mechanisms that contribute to mass REE resolubilization and selective sequestration are poorly understood. We have isolated bacteria (Bacillus mycoides JR07 and Bacillus pseudomycoides KB7) that solubilize Mn oxide, La oxide, and AMD solids by acidogenesis. Preliminary results show methylotrophic bacterial isolate B3 can take up soluble La, which may have a potential application in the purification of La from a mixed REE leachate. Determining the microbial metabolism and genes involved in the REE resolubilization and selective biomining of La is crucial to optimize the biomining of AMD solids. Our work addresses the growing need to develop novel REE recovery methods from domestic sources.
Phytoplankton account for nearly half of global photosynthetic carbon fixation, and the fate of that carbon is regulated in large part by microbial food web processing. We currently lack a mechanistic understanding of how interactions among heterotrophic bacteria impact the fate of photosynthetically fixed carbon. Here, we used a set of bacterial isolates capable of growing on exudates from the diatom Phaeodactylum tricornutum to investigate how bacteria-bacteria interactions affect the balance between exudate remineralization and incorporation into biomass. With exometabolomics and genome-scale metabolic modeling, we estimated the degree of resource competition between bacterial pairs. In a sequential spent media experiment, we found that pairwise interactions were more beneficial than predicted based on resource competition alone, and 30% exhibited facilitative interactions. To link this to carbon fate, we used single-cell isotope tracing in a custom cultivation system to compare the impact of different "primary" bacterial strains in close proximity to live P. tricornutum on a distal "secondary" strain. We found that a primary strain with a high degree of competition decreased secondary strain carbon drawdown by 51% at the single-cell level, providing a quantitative metric for the "cost" of competition on algal carbon fate. Additionally, a primary strain classified as facilitative based on sequential interactions increased total algal-derived carbon assimilation by 7.6 times, integrated over all members, compared to the competitive primary strain. Our findings suggest that the degree of interaction between bacteria along a spectrum from competitive to facilitative is directly linked to algal carbon drawdown.
Microbial genomes produced by standard single-cell amplification methods are largely incomplete. Here, we show that primary template-directed amplification (PTA), a novel single-cell amplification technique, generated nearly complete genomes from three bacterial isolate species. Furthermore, taxonomically diverse genomes recovered from aquatic and soil microbiomes using PTA had a median completeness of 81%, whereas genomes from standard multiple displacement amplification-based approaches were usually <30% complete. PTA-derived genomes also included more associated viruses and biosynthetic gene clusters.
The role of microbial necromass (nonliving microbial biomass), a significant component of belowground organic carbon, in nutrient cycling and its impact on the dynamics of microbial communities in subsurface systems remains poorly understood. It is currently unclear whether necromass metabolites from various microbes are different, whether certain groups of metabolites are preferentially utilized over others, or whether different microbial species respond to various necromass metabolites. In this study, we aimed to fill these knowledge gaps by designing enrichments with necromass as the sole nutrient source for subsurface microbial communities. We used the soluble fraction of necromass from bacterial isolates belonging to Arthrobacter, Agrobacterium, and Pseudomonas genera, and our results indicate that metabolite composition of necromass varied slightly across different strains but generally included amino acids, organic acids, and nucleic acid constituents. Arthrobacter-derived necromass appeared more recalcitrant. Necromass metabolites enriched diverse microbial genera, particularly Massilia sp. responded quickly regardless of the necromass source. Despite differences in necromass utilization, microbial community composition converged rapidly over time across the three different necromass amendments. Uracil, xanthine, valine, and phosphate-containing isomers were generally depleted over time, indicating microbial assimilation for maintenance and growth. However, numerous easily assimilable metabolites were not significantly depleted, suggesting efficient necromass recycling and the potential for necromass stabilization in systems. This study highlights the dynamic interactions between microbial necromass metabolites and subsurface microbial communities, revealing both selective utilization and rapid community and necromass convergence regardless of the necromass source.
The rhizosphere constitutes a dynamic interface between plant hosts and their associated microbial communities. Despite the acknowledged potential for enhancing plant fitness by manipulating the rhizosphere, the engineering of the rhizosphere microbiome through inoculation has posed significant challenges. These challenges are thought to arise from the competitive microbial ecosystem where introduced microbes must survive, and the absence of adaptation to the specific metabolic and environmental demands of the rhizosphere. Here, in this study, we engineered a synthetic rhizosphere community (SRC1) with the anticipation that it would exhibit a selective advantage in colonizing the host Sorghum bicolor, thereby potentially fostering its growth. SRC1 was assembled from bacterial isolates identified either for their potential role in community cohesion through network analysis or for their ability to benefit from host-specific exudate compounds. The growth performance of SRC1 was assessed in vitro on solid media, in planta under gnotobiotic laboratory conditions, and in the field. Our findings reveal that SRC1 cohesion is most robust when cultivated in the presence of the plant host under laboratory conditions, with lineages being lost from the community when grown either in vitro or in a native field setting. We establish that SRC1 effectively promotes the growth of both above- and below-ground plant phenotypes in both laboratory and native field contexts. Furthermore, in laboratory conditions, these growth enhancements correlate with the transcriptional dampening of lignin biosynthesis in the host. Collectively, these results underscore the potential utility of synthetic microbial communities for modulating crop performance in controlled and native environments alike.
Anthropogenic perturbations to the nitrogen cycle, primarily through use of synthetic fertilizers, is driving an unprecedented increase in the emission of nitrous oxide (N 2 O), a potent greenhouse gas and an ozone depleting substance, causing urgency in identifying the sources and sinks of N 2 O. Microbial denitrification is a primary contributor to biotic production of N 2 O in anoxic regions of soil, marine systems, and wastewater treatment facilities. Here, through comprehensive genome analysis, we show that pathway partitioning is a ubiquitous mechanism of complete denitrification within microbial communities. We have investigated mechanisms and consequences of process partitioning of denitrification through detailed physiological characterization and kinetic modeling of a synthetic community of Rhodanobacter thiooxydans FW510-R12 and Acidovorax sp. GW101-3H11. We have discovered that these two bacterial isolates, from a heavily nitrate (NO 3 − ) contaminated superfund site, complete denitrification through the exchange of nitrite (NO 2 − ) and nitric oxide (NO). The process partitioning of denitrification and other processes, including amino acid metabolism, contribute to increased cooperativity within this denitrifying community. We demonstrate that certain contexts, such as high NO 3 − , cause unbalanced growth of community members, due to differences in their substrate utilization kinetics. The altered growth characteristics of community members drives accumulation of toxic NO 2 − , which disrupts denitrification causing N 2 O off gassing.
We present the genome assemblies of two similar Paeniglutamicibacter strains, ORCA_105 and MACA_103, isolated from Mammoth and Oregon Cave systems, respectively. These closely related, but distinct genomes will provide a resource for those studying genomic adaptation to caves.