Comparison of microbial community assemblages in the rhizosphere of three Amaranthus spp.

Weed management remains a major challenge in cropping systems worldwide, with rising interest in ecological based approaches that can be integrated with herbicide use. Soil microbial communities may play important, yet undiscovered, roles in weed success. Little is known about the rhizosphere communities associated with weeds like Amaranthus, commonly known as pigweeds, and considered some of the most problematic weeds in agricultural systems. In a greenhouse experiment that allowed controlled plant growth conditions and a high number of individual plant specimens to analyze for statistical robustness (n = 8 per species), we show that specific bacterial assemblages form in the rhizospheres of A. retroflexus L. (redroot pigweed), A. palmeri S. Watson (Palmer amaranth), and A. tuberculatus (Moq.) J. D. Sauer (waterhemp). Using a relatively rapid and easy approach of T-RFLP community profiling of the 16S rRNA genes, distinct assemblages corresponded to plant species (PERMANOVA F = 14.776, p = 0.001), and further within each species, similar communities (F = 11.449, p = 0.001) were associated with three rhizosphere soil fractions taken in increasing distances away from the root tissue. These results provide the first solid basis for distinct plant-microbe relationships within three closely related Amaranthus species, warranting closer examination of the identities and function of the microorganisms that appear to be selectively recruited from the extant soil community. More intensive efforts to obtain the microbial taxonomic identities via sequencing are underway that can lead to further detailed studies to elucidate important functional plant-microbe interactions that may associate with weed success. Such data provides underlying key information that may ultimately exploit weed-microbe interactions in development of new integrated weed control tactics.

Tropical lacustrine sediment microbial community response to an extreme El Niño event.

Salinity can influence microbial communities and related functional groups in lacustrine sediments, but few studies have examined temporal variability in salinity and associated changes in lacustrine microbial communities and functional groups. To better understand how microbial communities and functional groups respond to salinity, we examined geochemistry and functional gene amplicon sequence data collected from 13 lakes located in Kiritimati, Republic of Kiribati (2° N, 157° W) in July 2014 and June 2019, dates which bracket the very large El Niño event of 2015-2016 and a period of extremely high precipitation rates. Lake water salinity values in 2019 were significantly reduced and covaried with ecological distances between microbial samples. Specifically, phylum- and family-level results indicate that more halophilic microorganisms occurred in 2014 samples, whereas more mesohaline, marine, or halotolerant microorganisms were detected in 2019 samples. Functional Annotation of Prokaryotic Taxa (FAPROTAX) and functional gene results (nifH, nrfA, aprA) suggest that salinity influences the relative abundance of key functional groups (chemoheterotrophs, phototrophs, nitrogen fixers, denitrifiers, sulfate reducers), as well as the microbial diversity within functional groups. Accordingly, we conclude that microbial community and functional gene groups in the lacustrine sediments of Kiritimati show dynamic changes and adaptations to the fluctuations in salinity driven by the El Niño-Southern Oscillation.

Stable carbon isotope values of syndepositional carbonate spherules and micrite record spatial and temporal changes in photosynthesis intensity.

Marine and lacustrine carbonate minerals preserve carbon cycle information, and their stable carbon isotope values (δ13 C) are frequently used to infer and reconstruct paleoenvironmental changes. However, multiple processes can influence the δ13 C values of bulk carbonates, confounding the interpretation of these values in terms of conditions at the time of mineral precipitation. Co-existing carbonate forms may represent different environmental conditions, yet few studies have analyzed δ13 C values of syndepositional carbonate grains of varying morphologies to investigate their origins. Here, we combine stable isotope analyses, metagenomics, and geochemical modeling to interpret δ13 C values of syndepositional carbonate spherules (>500 µm) and fine-grained micrite (<63 µm) from a ~1600-year-long sediment record of a hypersaline lake located on the coral atoll of Kiritimati, Republic of Kiribati (1.9°N, 157.4°W). Petrographic, mineralogic, and stable isotope results suggest that both carbonate fractions precipitate in situ with minor diagenetic alterations. The δ13 C values of spherules are high compared to the syndepositional micrite and cannot be explained by mineral differences or external perturbations, suggesting a role for local biological processes. We use geochemical modeling to test the hypothesis that the spherules form in the surface microbial mat during peak diurnal photosynthesis when the δ13 C value of dissolved inorganic carbon is elevated. In contrast, we hypothesize that the micrite may precipitate more continuously in the water as well as in sub-surface, heterotrophic layers of the microbial mat. Both metagenome and geochemical model results support a critical role for photosynthesis in influencing carbonate δ13 C values. The down-core spherule-micrite offset in δ13 C values also aligns with total organic carbon values, suggesting that the difference in the δ13 C values of spherules and micrite may be a more robust, inorganic indicator of variability in productivity and local biological processes through time than the δ13 C values of individual carbonate forms.

Refined NrfA phylogeny improves PCR-based nrfA gene detection.

Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are contrasting microbial processes in the terrestrial nitrogen (N) cycle, in that the former promotes N retention and the latter leads to N loss (i.e., the formation of gaseous products). The nitrite reductase NrfA catalyzes nitrite reduction to ammonium, the enzyme associated with respiratory nitrite ammonification and the key step in DNRA. Although well studied biochemically, the diversity and phylogeny of this enzyme had not been rigorously analyzed. A phylogenetic analysis of 272 full-length NrfA protein sequences distinguished 18 NrfA clades with robust statistical support (>90% Bayesian posterior probabilities). Three clades possessed a CXXCH motif in the first heme-binding domain, whereas all other clades had a CXXCK motif in this location. The analysis further identified a KXRH or KXQH motif between the third and fourth heme-binding motifs as a conserved and diagnostic feature of all pentaheme NrfA proteins. PCR primers targeting a portion of the heme-binding motifs that flank this diagnostic region yielded the expected 250-bp-long amplicons with template DNA from eight pure cultures and 16 new nrfA-containing isolates. nrfA amplicons obtained with template DNA from two geomorphically distinct agricultural soils could be assigned to one of the 18 NrfA clades, providing support for this expanded classification. The extended NrfA phylogeny revealed novel diagnostic features of DNRA populations and will be useful to assess nitrate/nitrite fate in natural and engineered ecosystems.

Efficacy of anal fistula plug in closure of cryptoglandular fistulas: long-term follow-up.

PURPOSE: The long-term efficacy of Surgisis anal fistula plug in closure of cryptoglandular anorectal fistulas was studied. METHODS: Patients with high cryptoglandular anorectal fistulas were prospectively studied. Additional variables recorded were: number of fistula tracts, and presence of setons. Under general anesthesia and in prone jackknife position, patients underwent irrigation of the fistula tract by using hydrogen peroxide. Each primary opening was occluded by using a Surgisis anal fistula plug, which was securely sutured in place at the primary opening and tacked to the periphery of the secondary opening. RESULTS: Forty-six patients were prospectively enrolled during a two-year period. Follow-up was six months to two years (median, 12 months). At final follow-up, all fistula tracts had been successfully closed in 38 patients, for an overall success rate of 83 percent. Seven patients had multiple tracts, for a total of 55 fistula tracts in the series. Of the 55 individual tracts, 47 (85 percent) were closed at final follow-up. Patients with one primary opening were most likely to have successful closure by using the anal fistula plug, although this was not significant. Successful closure was not correlated with the presence of setons. CONCLUSIONS: Long-term closure of cryptoglandular anorectal fistula tracts using Surgisis anal fistula plug is safe and successful in 83 percent of patients and 85 percent of tracts.