Sterile sentinels and MinION sequencing capture active soil microbial communities that differentiate crop rotations.

BACKGROUND: Soil microbial communities are difficult to measure and critical to soil processes. The bulk soil microbiome is highly diverse and spatially heterogeneous, which can make it difficult to detect and monitor the responses of microbial communities to differences or changes in management, such as different crop rotations in agricultural research. Sampling a subset of actively growing microbes should promote monitoring how soil microbial communities respond to management by reducing the variation contributed by high microbial spatial and temporal heterogeneity and less active microbes. We tested an in-growth bag method using sterilized soil in root-excluding mesh, "sterile sentinels," for the capacity to differentiate between crop rotations. We assessed the utility of different incubation times and compared colonized sentinels to concurrently sampled bulk soils for the statistical power to differentiate microbial community composition in low and high diversity crop rotations. We paired this method with Oxford Nanopore MinION sequencing to assess sterile sentinels as a standardized, fast turn-around monitoring method. RESULTS: Compared to bulk soil, sentinels provided greater statistical power to distinguish between crop rotations for bacterial communities and equivalent power for fungal communities. The incubation time did not affect the statistical power to detect treatment differences in community composition, although longer incubation time increased total biomass. Bulk and sentinel soil samples contained shared and unique microbial taxa that were differentially abundant between crop rotations. CONCLUSIONS: Overall, compared to bulk soils, the sentinels captured taxa with copiotrophic or ruderal traits, and plant-associated taxa. The sentinels show promise as a sensitive, scalable method to monitor soil microbial communities and provide information complementary to traditional soil sampling.

Long term crop rotation effect on subsequent soybean yield explained by soil and root-associated microbiomes and soil health indicators.

Crop rotation is an important management tactic that farmers use to manage crop production and reduce pests and diseases. Long-term crop rotations may select groups of microbes that form beneficial or pathogenic associations with the following crops, which could explain observed crop yield differences with different crop sequences. To test this hypothesis, we used two locations each with four long-term (12-14-year), replicated, rotation treatments: continuous corn (CCC), corn/corn/soybean (SCC), corn/soybean (CSC), and soybean/corn (SCS). Afterwards, soybean was planted, and yield and soil health indicators, bulk soil microbiome, and soybean root-associated microbiome were assessed. Soybean yields, as well as soil protein, and POXC as soil health indicators were higher following CCC than in the other three treatments at both locations. A bacterial taxon in family JG30-KF-AS9 was enriched in CCC, whereas Microvirga, Rhodomicrobium, and Micromonosporaceae were enriched in SCS. Several ascomycetes explain lowered yield as soybean pathogens in SCS. Surprisingly, Tumularia, Pyrenochaetopsis and Schizothecium were enriched in soybean roots after CCC, suggesting corn pathogens colonizing soybean roots as nonpathogens. Our finding of associations between soil health indicators related to microbiomes and soybean yield has wide-ranging implications, opening the possibility of manipulating microbiomes to improve crop yield potential.

Addressing a national crisis: the spine hospital and department's response to the COVID-19 pandemic in New York City.

In a very brief period, the COVID-19 pandemic has swept across the planet leaving governments, societies, and healthcare systems unprepared and under-resourced. New York City now represents the global viral epicenter with roughly one-third of all mortalities in the United States. To date, our hospital has treated thousands of COVID-19 positive patients and sits at the forefront of the United States response to this pandemic. The goal of this paper is to share the lessons learned by our spine division during a crisis when hospital resources and personnel are stretched thin. Such experiences include management of elective and emergent cases, outpatient clinics, physician redeployment, and general health and wellness. As peak infections spread across the United States, we hope this article will serve as a resource for other spine departments on how to manage patient care and healthcare worker deployment during the COVID-19 crisis.

Comparative measurements of arbuscular mycorrhizal fungal responses to agricultural management practices.

Arbuscular mycorrhizal (AM) fungi are considered to be a key group of soil organisms for assessments of soil biological properties and developing relationships among crop production management practices, soil properties, crop performance, and ecosystem services. In a field study of cover crop treatments established during the transition from small grains to corn (Zea mays L), we assessed multiple measures of AM fungal responses to the management treatments: soil propagule numbers, biomass via lipid biomarkers, and root colonization extent. Our objectives were to determine response variables that reliably distinguished cover crop treatments and formed consistent relationships with grain yield, plant biomass, and mineral nutrient concentrations of the following corn crop. The number of soil AM fungal propagules and amount of the NLFA biomarker C16:1cis11 measured on fall-collected soils most consistently and significantly responded to fall cover crop treatments. Neither of these measures of soil inoculum potential was strongly related to measures of crop performance. The PLFA biomarker C16:1cis11 was marginally responsive to cover crop but did not strongly relate to crop performance parameters. Corn root colonization by AM fungi was not significantly affected by cover crop treatment, but significant negative relationships were found between root colonization and grain N concentration and plant biomass at maturity. In contrast, a significant positive relationship between root colonization and plant N concentration at the 6-leaf stage was found. Understanding the relative effectiveness and limitations of AM fungal response variables will inform their application in field studies of agricultural management practices.

OPTN/SRTR 2017 Annual Data Report: Lung.

Each year since 2012, the number of lung transplants has increased, reflecting an increase in the number of donors, improved use of recovered organs, and more candidates being listed for transplant. However, the need for organs continues to outpace available donors. Despite an increase of 126 donors in 2017, 1360 candidates remained on the waiting list at the end of the year, and 326 patients died or became too sick to undergo transplant. Approximately 14,000 individuals were living with a lung transplant in 2017; 9492 were aged 50 years or older, 4075 were aged 18-49 years, and 408 were aged younger than 18 years.

OPTN/SRTR 2017 Annual Data Report: Heart.

In 2017, 3273 heart transplants were performed in the United States. New listings continued to increase, and 3769 new adults were listed for heart transplant in 2017. Over the past decade, posttransplant mortality has declined. The number of new pediatric listings increased over the past decade, as did the number of pediatric heart transplants, although some fluctuation has occurred more recently. New listings for pediatric heart transplants increased from 481 in 2007 to 623 in 2017. The number of pediatric heart transplants performed each year increased from 330 in 2007 to 432 in 2017, slightly fewer than in 2016. Short-term and long-term mortality improved. Among pediatric patients who underwent transplant between 2015-2016, 4.8% had died by 6 months and 6.2% by 1 year.

Response of Soil Surface Greenhouse Gas Fluxes to Crop Residue Removal and Cover Crops under a Corn-Soybean Rotation.

Excessive crop residue returned to the soil hinders farm operations, but residue removal can affect soil quality. In contrast, cover cropping can return additional residue to the soil and improve soils and environmental quality compared with no cover cropping. Residue and cover crop impacts on soil surface greenhouses gas (GHG) emissions are undetermined and site specific. Thus, the present study was conducted to investigate the impacts of corn ( L.) residue management and cover cropping on GHG fluxes. The fluxes were measured from 2013 to 2015 using static chamber under corn and soybean [ (L.) Merr.] rotation initiated in 2000 at Brookings, SD. Treatments included two residue management levels (residue returned [RR] and residue not returned [RNR]) and two cover cropping (cover crops [CC] and no cover crops [NCC]). Results showed that RR under corn and soybean phases significantly reduced cumulative CO fluxes (2681.3 kg ha in corn and 2419.8 kg ha in soybeans) compared with RNR (3331.0 kg ha in corn and 2755.0 kg ha in soybeans) in 2013. The RR emitted significantly less cumulative NO fluxes than RNR from both the phases in 2013 and 2014, but not in 2015. The CC treatment had significantly lower cumulative NO fluxes than the NCC for corn and soybean phases in 2013 and 2014. We conclude that crop residue retention and cover cropping can mitigate the GHG emissions compared with residue removal and no cover cropping.

Measuring and monitoring equity in access to deceased donor kidney transplantation.

The Organ Procurement and Transplantation Network monitors progress toward strategic goals such as increasing the number of transplants and improving waitlisted patient, living donor, and transplant recipient outcomes. However, a methodology for assessing system performance in providing equity in access to transplants was lacking. We present a novel approach for quantifying the degree of disparity in access to deceased donor kidney transplants among waitlisted patients and determine which factors are most associated with disparities. A Poisson rate regression model was built for each of 29 quarterly, period-prevalent cohorts (January 1, 2010-March 31, 2017; 5 years pre-kidney allocation system [KAS], 2 years post-KAS) of active kidney waiting list registrations. Inequity was quantified as the outlier-robust standard deviation (SDw ) of predicted transplant rates (log scale) among registrations, after "discounting" for intentional, policy-induced disparities (eg, pediatric priority) by holding such factors constant. The overall SDw declined by 40% after KAS implementation, suggesting substantially increased equity. Risk-adjusted, factor-specific disparities were measured with the SDw after holding all other factors constant. Disparities associated with calculated panel-reactive antibodies decreased sharply. Donor service area was the factor most associated with access disparities post-KAS. This methodology will help the transplant community evaluate tradeoffs between equity and utility-centric goals when considering new policies and help monitor equity in access as policies change.

OPTN/SRTR 2016 Annual Data Report: Lung.

In 2016, 2692 candidates aged 12 years or older were added to the lung transplant waiting list; 2345 transplants were performed, the largest number of any prior year. The median waiting time for listed candidates in 2016 was 2.5 months, and waiting times were shortest for group D candidates. The transplant rate increased to 191.9 transplants per 100 waitlist years in 2016, with a slight decrease in waitlist mortality to 15.1 deaths per 100 waitlist years. Short-term survival continued to improve, with a 6-month death rate of 6.6% and a 1-year death rate of 10.8% among recipients in 2015 compared with 8.0% and 13.3%, respectively, among recipients in 2014. Long-term survival rates remained unchanged; 55.6% of recipients were alive at 5 years. In 2016, 23 new candidates aged 0-11 years were added to the waiting list and 16 lung transplants were performed. Incidence of posttransplant mortality for lung transplant recipients aged 0-11 years who underwent transplant in 2014-2015 was 13.8% at 6 months and 19.6% at 1 year. Changes in waitlist and transplant demographic features continued to evolve following implementation of the revised lung allocation score in 2015. Some early trends that may be attributable to the revised LAS are shorter waiting times, stabilization of the number of group D candidates listed for transplant, and convergence of LAS with lower prevalence of extremely high scores.

OPTN/SRTR 2016 Annual Data Report: Heart.

In 2016, 3209 heart transplants were performed in the United States. New, active listings increased 57% since 2005. The number of adult heart transplant survivors continued to increase, and in 2016, 30,622 recipients were living with heart transplants. Patient mortality following transplant has declined. The number of pediatric candidates and transplants performed also increased. New listings for pediatric heart transplants increased from 454 in 2005 to 624 in 2016. The number of pediatric heart transplants performed each year increased from 319 in 2005 to 445 in 2016. Among pediatric patients who underwent transplant in 2015, death occurred in 5.9% at 6 months and 7.2% at 1 year.

Previous crop and rotation history effects on maize seedling health and associated rhizosphere microbiome.

To evaluate crop rotation effects on maize seedling performance and its associated microbiome, maize plants were grown in the greenhouse in soils preceded by either maize, pea, soybean or sunflower. Soils originated from a replicated field experiment evaluating different four-year rotation combinations. In the greenhouse, a stressor was introduced by soil infestation with western corn rootworm (WCR) or Fusarium graminearum. Under non-infested conditions, maize seedlings grown in soils preceded by sunflower or pea had greater vigor. Stress with WCR or F. graminearum resulted in significant root damage. WCR root damage was equivalent for seedlings regardless of soil provenance; whereas F. graminearum root damage was significantly lower in maize grown in soils preceded by sunflower. Infestation with WCR affected specific microbial taxa (Acinetobacter, Smaragdicoccus, Aeromicrobium, Actinomucor). Similarly, F. graminearum affected fungal endophytes including Trichoderma and Endogone. In contrast to the biological stressors, rotation sequence had a greater effect on rhizosphere microbiome composition, with larger effects observed for fungi compared to bacteria. In particular, relative abundance of Glomeromycota was significantly higher in soils preceded by sunflower or maize. Defining the microbial players involved in crop rotational effects in maize will promote selection and adoption of favorable crop rotation sequences.

Sex-specific interactions of microbial symbioses on cricket dietary selection.

The nutrients found in prey and nonprey foods, and relative digestibility of these foods, has a major influence on diet selection by omnivorous insects. Many insects have developed symbiotic relationships with gut bacteria to help with extracting nutrition from nonprey diets. Gryllus pennsylvanicus (Burmeister) (Orthoptera: Gryllidae) was assigned to one of two treatment groups, antibiotic-treated and nonantibiotic-treated, and consumption of seeds (nonprey) and eggs (prey) were measured. Male crickets administered antibiotics consumed more seeds and greater seed weight, while antibiotic-fed female crickets consumed fewer seeds and less seed weight, relative to the untreated male and female crickets, respectively. Both male and female antibiotic-treated crickets consumed similar weight of eggs as nonantibiotic-treated male and female crickets, respectively. These results provide evidence that gut symbionts influence diet selection of male and female G. pennsylvanicus differently. This sex-specific dietary selection may be because of the fact that male and female crickets have different nutritional requirements.

Aerobic stability of distillers wet grains as influenced by temperature.

BACKGROUND: The storability of distillers wet grains (DWG) influences the economic, energetic, and carbon balances of fuel ethanol production, yet there are limited published data on the deterioration of DWG following its production. We used biogenic CO(2) production to assess the aerobic stability of DWG incubated at three temperatures (12 °C, 22 °C, 32 °C) and compared CO(2) production over time to the appearance of mold and changes in DWG color parameters. RESULTS: CO(2) production and mold colonization indicate that at temperatures near 12 °C, the aerobic stability of DWG was high and that it can be stored for at least a 10-day period. At temperatures close to 22 °C, the onset of increased microbial activity and visible mold colonization occurred between 4 and 7 days and both activity and mold ratings were very high by the ninth day in all three experiments. At 32 °C, 2 days may be a more appropriate limit for storage. CONCLUSION: Temperature and time interact in a nonlinear fashion that permits the prediction of DWG stability boundaries. The simple visual appearance of mold appears to be a reasonable indicator that correlates well (r = 0.694) with CO(2) production, a measure of the aerobic stability of DWG.

Bacterial gut symbionts contribute to seed digestion in an omnivorous beetle.

BACKGROUND: Obligate bacterial symbionts alter the diets of host animals in numerous ways, but the ecological roles of facultative bacterial residents that colonize insect guts remain unclear. Carabid beetles are a common group of beneficial insects appreciated for their ability to consume insect prey and seeds, but the contributions of microbes to diet diversification in this and similar groups of facultative granivores are largely unknown. METHODOLOGY AND PRINCIPAL FINDINGS: Using 16S rRNA gene clone libraries and terminal restriction fragment (tRF) length polymorphism analyses of these genes, we examined the bacterial communities within the guts of facultatively granivorous, adult Harpalus pensylvanicus (Carabidae), fed one of five dietary treatments: 1) an untreated Field population, 2) Seeds with antibiotics (seeds were from Chenopodium album), 3) Seeds without antibiotics, 4) Prey with antibiotics (prey were Acheta domesticus eggs), and 5) Prey without antibiotics. The number of seeds and prey consumed by each beetle were recorded following treatment. Harpalus pensylvanicus possessed a fairly simple gut community of approximately 3-4 bacterial operational taxonomic units (OTU) per beetle that were affiliated with the Gammaproteobacteria, Bacilli, Alphaproteobacteria, and Mollicutes. Bacterial communities of the host varied among the diet and antibiotic treatments. The field population and beetles fed seeds without antibiotics had the closest matching bacterial communities, and the communities in the beetles fed antibiotics were more closely related to each other than to those of the beetles that did not receive antibiotics. Antibiotics reduced and altered the bacterial communities found in the beetle guts. Moreover, beetles fed antibiotics ate fewer seeds, and those beetles that harbored the bacterium Enterococcus faecalis consumed more seeds on average than those lacking this symbiont. CONCLUSIONS/SIGNIFICANCE: We conclude that the relationships between the bacterium E. faecalis and this factultative granivore's ability to consume seeds merit further investigation, and that facultative associations with symbiotic bacteria have important implications for the nutritional ecology of their hosts.

Response of coccidiostat- versus vaccination-protected broilers to gelatin inclusion in high and low crude protein diets.

Experimentation examined if Gly and Ser (Gly + Ser) and Pro from gelatin inclusion in low and high CP feeds would relieve impaired performance of broilers after vaccination for coccidiosis. Broilers in floor pens were fed 20-18-16% or 23-20-18% CP corn-soybean meal regimens from 0 to 8 wk of age such that 1 or more of the most limiting essential amino acid levels were similar across treatments and considered adequate respective of age. Gelatin was included in diets at 2%, which contributed Gly + Ser and Pro levels comparable to using 5% meat meal. Half of the chicks were spray-vaccinated with live oocysts before placement and received nonmedicated feed, whereas the other half received coccidiostat-medicated (salinomycin) feed to 6 wk of age. Vaccination adversely affected live performance in the first 3 wk, which could not be fully compensated to the level of birds receiving coccidiostat by the end of experimentation. Inclusion of gelatin mitigated vaccination response through the first 3 wk, while improving overall live performance of birds fed low CP diets. Gelatin had no effect on carcass composition, but the low CP regimen increased abdominal fat and reduced carcass and breast meat relative to high CP feeds. Vaccination also reduced overall carcass weight; however, part yields were not affected. Males were generally more sensitive to treatments than females. The conditionally essential amino acids Gly + Ser and Pro may be important factors in recovery from live anticoccidial vaccines.

Bacterial communities associated with the digestive tract of the predatory ground beetle, Poecilus chalcites, and their modification by laboratory rearing and antibiotic treatment.

Ground beetles such as Poecilus chalcites (Coleoptera: Carabidae) are beneficial insects in agricultural systems where they contribute to the control of insect and weed pests. We assessed the complexity of bacterial communities occurring in the digestive tracts of field-collected P. chalcites using terminal restriction fragment length polymorphism analyses of polymerase chain reaction-amplified 16S rRNA genes. Bacterial identification was performed by the construction of 16S rRNA gene clone libraries and sequence analysis. Intestinal bacteria in field-collected beetles were then compared to those from groups of beetles that were reared in the lab on an artificial diet with and without antibiotics. Direct cell counts estimated 1.5x10(8) bacteria per milliliter of gut. The digestive tract of field-collected P. chalcites produced an average of 4.8 terminal restriction fragments (tRF) for each beetle. The most abundant clones were affiliated with the genus Lactobacillus, followed by the taxa Enterobacteriaceae, Clostridia, and Bacteriodetes. The majority of the sequences recovered were closely related to those reported from other insect gastrointestinal tracts. Lab-reared beetles produced fewer tRF, an average of 3.1 per beetle, and a reduced number of taxa with a higher number of clones from the family Enterobacteriaceae compared to the field-collected beetles. Antibiotic treatment significantly (p<0.05) reduced the number of tRF per beetle and selected for a less diverse set of bacterial taxa. We conclude that the digestive tract of P. chalcites is colonized by a simple community of bacteria that possess autochthonous characteristics. Laboratory-reared beetles harbored the most common bacteria found in field-collected beetles, and these bacterial communities may be manipulated in the laboratory with the addition of antibiotics to the diet to allow study of functional roles.

Microbial development in distillers wet grains produced during fuel ethanol production from corn (Zea mays).

Distillers grains are coproduced with ethanol and carbon dioxide during the production of fuel ethanol from the dry milling and fermentation of corn grain, yet there is little basic microbiological information on these materials. We undertook a replicated field study of the microbiology of distillers wet grains (DWG) over a 9 day period following their production at an industrial fuel ethanol plant. Freshly produced DWG had a pH of about 4.4, a moisture content of about 53.5% (wet mass basis), and 4 x 10(5) total yeast cells/g dry mass, of which about 0.1% were viable. Total bacterial cells were initially below detection limits (ca. 10(6) cells/g dry mass) and then were estimated to be approximately 5 x 10(7) cells/g dry mass during the first 4 days following production. Culturable aerobic heterotrophic organisms (fungi plus bacteria) ranged between 10(4) and 10(5) CFU/g dry mass during the initial 4 day period, and lactic acid bacteria increased from 36 to 10(3) CFU/g dry mass over this same period. At 9 days, total viable bacteria and yeasts and (or) molds topped 10(8) CFU/g dry mass and lactic acid bacteria approached 10(6) CFU/g dry mass. Community phospholipid fatty acid analysis indicated a stable microbial community over the first 4 days of storage. Thirteen morphologically distinct isolates were recovered, of which 10 were yeasts and molds from 6 different genera, 2 were strains of the lactic-acid-producing Pediococcus pentosaceus and only one was an aerobic heterotrophic bacteria, Micrococcus luteus. The microbiology of DWG is fundamental to the assessment of spoilage, deleterious effects (e.g., toxins), or beneficial effects (e.g., probiotics) in its use as feed or in alternative applications.