Archaeal anaerobic methanotrophs (“ANME”) and sulfate-reducing Deltaproteobacteria (“SRB”) form symbiotic multicellular consortia capable of anaerobic methane oxidation (AOM), and in so doing modulate methane flux from marine sediments. The specificity with which ANME associate with particular SRB partners in situ, however, is poorly understood. To characterize partnership specificity in ANME-SRB consortia, we applied the correlation inference technique SparCC to 310 16S rRNA amplicon libraries prepared from Costa Rica seep sediment samples, uncovering a strong positive correlation between ANME-2b and members of a clade of Deltaproteobacteria we termed SEEP-SRB1g. We confirmed this association by examining 16S rRNA diversity in individual ANME-SRB consortia sorted using flow cytometry and by imaging ANME-SRB consortia with fluorescence in situ hybridization (FISH) microscopy using newly-designed probes targeting the SEEP-SRB1g clade. Analysis of genome bins belonging to SEEP-SRB1g revealed the presence of a complete nifHDK operon required for diazotrophy, unusual in published genomes of ANME-associated SRB. Active expression of nifH in SEEP-SRB1g within ANME-2b—SEEP-SRB1g consortia was then demonstrated by microscopy using hybridization chain reaction (HCR-) FISH targeting nifH transcripts and diazotrophic activity was documented by FISH-nanoSIMS experiments. NanoSIMS analysis of ANME-2b—SEEP-SRB1g consortia incubated with a headspace containing CH4 and 15N2 revealed differences in cellular 15N-enrichment between the two partners that varied between individual consortia, with SEEP-SRB1g cells enriched in 15N relative to ANME-2b in one consortium and the opposite pattern observed in others, indicating both ANME-2b and SEEP-SRB1g are capable of nitrogen fixation, but with consortium-specific variation in whether the archaea or bacterial partner is the dominant diazotroph.
Microscopic and spectroscopic techniques are commonly applied to study microbial cells but are typically used on separate samples, resulting in population-level datasets that are integrated across different cells with little spatial resolution. To address this shortcoming, we developed a workflow that correlates several microscopic and spectroscopic techniques to generate an in-depth analysis of individual cells. By combining stable isotope probing (SIP), fluorescence in situ hybridization (FISH), scanning electron microscopy (SEM), confocal Raman microspectroscopy (Raman), and nano-scale secondary ion mass spectrometry (NanoSIMS), we illustrate how individual cells can be thoroughly interrogated to obtain information about their taxonomic identity, structure, physiology, and metabolic activity. Analysis of an artificial microbial community demonstrated that our correlative approach was able to resolve the activity of single cells using heavy water SIP in conjunction with Raman and/or NanoSIMS and establish their taxonomy and morphology using FISH and SEM. This workflow was then applied to a sample of yet uncultured multicellular magnetotactic bacteria (MMB). In addition to establishing their identity and activity, backscatter electron microscopy (BSE), NanoSIMS, and energy-dispersive X-ray spectroscopy (EDS) were employed to characterize the magnetosomes within the cells. By integrating these techniques, we demonstrate a cohesive approach to thoroughly study environmental microbes on a single-cell level.
more » « less- NSF-PAR ID:
- 10368308
- Publisher / Repository:
- Oxford University Press
- Date Published:
- Journal Name:
- ISME Communications
- Volume:
- 2
- Issue:
- 1
- ISSN:
- 2730-6151
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
more » « less
Abstract -
more » « less
Abstract Background Stable isotope probing (SIP) approaches are a critical tool in microbiome research to determine associations between species and substrates, as well as the activity of species. The application of these approaches ranges from studying microbial communities important for global biogeochemical cycling to host-microbiota interactions in the intestinal tract. Current SIP approaches, such as DNA-SIP or nanoSIMS allow to analyze incorporation of stable isotopes with high coverage of taxa in a community and at the single cell level, respectively, however they are limited in terms of sensitivity, resolution or throughput.
Results Here, we present an ultra-sensitive, high-throughput protein-based stable isotope probing approach (Protein-SIP), which cuts cost for labeled substrates by 50–99% as compared to other SIP and Protein-SIP approaches and thus enables isotope labeling experiments on much larger scales and with higher replication. The approach allows for the determination of isotope incorporation into microbiome members with species level resolution using standard metaproteomics liquid chromatography-tandem mass spectrometry (LC–MS/MS) measurements. At the core of the approach are new algorithms to analyze the data, which have been implemented in an open-source software (
https://sourceforge.net/projects/calis-p/ ). We demonstrate sensitivity, precision and accuracy using bacterial cultures and mock communities with different labeling schemes. Furthermore, we benchmark our approach against two existing Protein-SIP approaches and show that in the low labeling range used our approach is the most sensitive and accurate. Finally, we measure translational activity using18O heavy water labeling in a 63-species community derived from human fecal samples grown on media simulating two different diets. Activity could be quantified on average for 27 species per sample, with 9 species showing significantly higher activity on a high protein diet, as compared to a high fiber diet. Surprisingly, among the species with increased activity on high protein were severalBacteroides species known as fiber consumers. Apparently, protein supply is a critical consideration when assessing growth of intestinal microbes on fiber, including fiber-based prebiotics.Conclusions We demonstrate that our Protein-SIP approach allows for the ultra-sensitive (0.01 to 10% label) detection of stable isotopes of elements found in proteins, using standard metaproteomics data.
-
more » « less
Summary The activity of individual microorganisms can be measured within environmental samples by detecting uptake of isotope‐labelled substrates using nano‐scale secondary ion mass spectrometry (nanoSIMS). Recent studies have demonstrated that sample preparation can decrease13C and15N enrichment in bacterial cells, resulting in underestimates of activity. Here, we explore this effect with a variety of preparation types, microbial lineages and isotope labels to determine its consistency and therefore potential for correction. Specifically, we investigated the impact of different protocols for fixation, nucleic acid staining and catalysed reporter deposition fluorescence
in situ hybridization (CARD‐FISH) on >14 500 archaeal and bacterial cells (Methanosarcina acetivorans ,Sulfolobus acidocaldarius andPseudomonas putida ) enriched in13C,15N,18O,2H and/or34S. We found these methods decrease isotope enrichments by up to 80% – much more than previously reported – and that the effect varies by taxa, growth phase, isotope label and applied protocol. We make recommendations for how to account for this effect experimentally and analytically. We also re‐evaluate published nanoSIMS datasets and revise estimated microbial turnover times in the marine subsurface and nitrogen fixation rates in pelagic unicellular cyanobacteria. When sample preparation is accounted for, cell‐specific rates increase and are more consistent with modelled and bulk rates. -
more » « less
Nanosphere lithography (NSL) is a bottom‐up, self‐assembly approach that enables rapid, low‐cost patterning of nanoscale features. The practical application and scalability of NSL relies on the ability to achieve defect‐free nanosphere self‐assembly over large substrate areas. Self‐assembly methods for single‐layer nanosphere templates are typically evaluated using scanning electron microscopy (SEM) imaging, with literature reports focusing on maximum area of continuous nanosphere coverage. An alternative performance metric—namely, the percentage of nanospheres exhibiting perfect hexagonal close‐packing (%HCP)—is uniquely critical to NSL precision and repeatability. To enhance current methods of evaluating nanosphere self‐assembly, this work presents an SEM image analysis approach for rapidly quantifying packing defects in single‐layer nanospheres to determine %HCP. The method uses variations in SEM edge effect brightness to distinguish spheres with perfect packing from those in defect configurations or along edges. Comparison of image analysis program results with manual counting of nanospheres indicates that the program has a high degree of accuracy, with a mean error on the %HCP metric of +8.6% (absolute error). The results suggest that the present strategy offers a promising pathway to rapid evaluation of nanosphere self‐assembly for high‐precision NSL applications such as surface‐enhanced Raman scattering, photovoltaic cells, and nanogap electrodes.
-
This article belongs to the Special Issue Synthesis and Applications of Gold Nanoparticles) Rodolphe Antoine (Ed.)more » « less
This research focuses on the plant-mediated green synthesis process to produce gold nanoparticles (Au NPs) using upland cress (Barbarea verna), as various biomolecules within the upland cress act as both reducing and capping agents. The synthesized gold nanoparticles were thoroughly characterized using UV-vis spectroscopy, surface charge (zeta potential) analysis, scanning electron microscopy-energy-dispersive X-ray spectroscopy (SEM-EDX), atomic force microscopy (AFM), attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR), and X-ray diffraction (XRD). The results indicated the synthesized Au NPs are spherical and well-dispersed with an average diameter ~11 nm and a characteristic absorbance peak at ~529 nm. EDX results showed an 11.13% gold content. Colloidal Au NP stability was confirmed with a zeta potential (ζ) value of −36.8 mV. X-ray diffraction analysis verified the production of crystalline face-centered cubic gold. Moreover, the antimicrobial activity of the Au NPs was evaluated using Gram-negative Escherichiacoli and Gram-positive Bacillus megaterium. Results demonstrated concentration-dependent antimicrobial properties. Lastly, applications of the Au NPs in catalysis and biomedicine were evaluated. The catalytic activity of Au NPs was demonstrated through the conversion of 4-nitrophenol to 4-aminophenol which followed first-order kinetics. Cellular uptake and cytotoxicity were evaluated using both BMSCs (stem) and HeLa (cancer) cells and the results were cell type dependent. The synthesized Au NPs show great potential for various applications such as catalysis, pharmaceutics, and biomedicine.
