Streptomyces apricus sp. nov., isolated from soil.

A novel Streptomyces strain, SUN51T, was isolated from soils sampled in Wisconsin, USA, as part of a Streptomyces biogeography survey. Genome sequencing revealed that this strain had less than 90 % average nucleotide identity (ANI) to type species of Streptomyces: SUN51T was most closely related to Streptomyces dioscori A217T (99.5 % 16S rRNA gene identity, 89.4 % ANI). Genome size was estimated at 8.81 Mb, and the genome DNA G+C content was 72 mol%. The strain possessed the cellular fatty acids anteiso-C15 : 0, iso-C16 : 0, 16 : 1 ω7c, anteiso-C17 : 0, iso-C14 : 0 and C16 : 0. The predominant menaquinones were MK-9 H4, MK-9 H6 and MK-9 H8. Strain SUN51T contained the polar lipids phosphatidic acid, phosphatidyl ethanolamine, phosphatidyl glycerol and diphosphatidyl glycerol. The cell wall contained ll-diaminopimelic acid. The strain could grow on a broad range of carbon sources and tolerate temperatures of up to 40 °C. The results of the polyphasic study confirmed that this isolate represents a novel species of the genus Streptomyces, for which the name Streptomyces apricus sp. nov. is proposed. The type strain of this species is SUN51T (=NRRL B-65543T=JCM 33736T).

Cultivated Sub-Populations of Soil Microbiomes Retain Early Flowering Plant Trait.

The collection of microorganisms found in the root zone of soil, termed the rhizosphere microbiome, has been shown to impact plant growth and development. Here, we tease apart the function of the cultivable portion of the microbiome from the whole microbiome in retaining plant traits modified through artificial selection on flowering time. Specifically, the whole microbiome associated with earlier flowering time of Arabidopsis thaliana was cultivated on four types of solid media to create cultivated fractions of the microbiome. These cultivated microbiomes were subsequently preserved in glycerol, frozen, and revived to yield a portion of the cultivable fraction to compare (1) whole microbiome, (2) cultivable microbiome, and (3) revived, cultivable microbiome controls on early flowering time. Plants grown in soils inoculated with bacteria grown on 25 % Luria broth and 10 % tryptic soy agar retained the early flowering trait. An increase in leaf biomass with two of the cultivated microbiomes (49.4 and 38.5 %) contrasted the lowered biomass effect of the whole microbiome. Inoculation with the cultivated microbiomes that were cryopreserved in glycerol showed no effect on flowering time or leaf biomass. The results indicate that the cultivable portion of a plant's microbiome retains the early flowering effect in A. thaliana, but cryopreservation of the cultivated microbiomes disrupts the microbial effects on flowering time. Furthermore, the contrasting effects on leaf biomass (an indirect response from selection on early flowering time), seen with the whole microbiome versus the cultivable portion, suggests versatility in using cultivation methods to modify multiple traits of plants.

Effects of physical, chemical, and biological ageing on the mineralization of pine wood biochar by a Streptomyces isolate.

If biochar is to be used for carbon (C) management, we must understand how weathering or ageing affects biochar C mineralization. Here, we incubated aged and unaged eastern white pine wood biochar produced at 350 and 550°C with a Streptomyces isolate, a putative biochar-decomposing microbe. Ageing was accelerated via three different processes, namely, (a) physical ageing-subjecting biochar to alternating freeze-thaw and wet-dry cycles, (b) chemical ageing-treating biochar with concentrated hydrogen peroxide and (c) biological ageing-incubating biochar in the presence of nutrients and microorganisms. Elemental composition and surface chemistry (Fourier Transform Infrared spectroscopy) of biochar samples were compared before and after ageing. Biochar C mineralization between ageing treatments was significantly different in the case of 350°C biochar (p value = 0.03). Among the 350°C biochars, physical ageing resulted in the greatest increase (by 103%) in biochar C mineralization (p value = 0.05). However, in the case of 550°C biochar, ageing did not result in a significant change in biochar C mineralization (p value = 0.40). Biochar C mineralization was positively correlated with an increase in O/C ratio post-ageing (rs = 0.86, p value = 0.01). In the case of 350°C biochar, surface oxidation during ageing enhanced biochar degradation by the isolate. For 550°C biochar, however, ageing did not significantly increase biochar C mineralization, likely due to high condensed aromatic C content and lower surface oxidation during ageing. The results from our study suggest that low temperature aged biochar is more susceptible to biological degradation by soil microbes. These findings have implications for the use of biochar for long term C storage in soils.

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities.

Microbial communities might include distinct lineages of closely related organisms that complicate metagenomic assembly and prevent the generation of complete metagenome-assembled genomes (MAGs). Here we show that deep sequencing using long (HiFi) reads combined with Hi-C binning can address this challenge even for complex microbial communities. Using existing methods, we sequenced the sheep fecal metagenome and identified 428 MAGs with more than 90% completeness, including 44 MAGs in single circular contigs. To resolve closely related strains (lineages), we developed MAGPhase, which separates lineages of related organisms by discriminating variant haplotypes across hundreds of kilobases of genomic sequence. MAGPhase identified 220 lineage-resolved MAGs in our dataset. The ability to resolve closely related microbes in complex microbial communities improves the identification of biosynthetic gene clusters and the precision of assigning mobile genetic elements to host genomes. We identified 1,400 complete and 350 partial biosynthetic gene clusters, most of which are novel, as well as 424 (298) potential host-viral (host-plasmid) associations using Hi-C data.

Bacterial community composition of vermicompost-treated tomato rhizospheres.

Vermicompost application has been shown to promote plant growth, alter the rhizosphere microbiome, and suppress plant pathogens. These beneficial properties are often attributed to the activity of vermicompost-associated microorganisms. However, little is known about the microbial shifts that occur in the rhizosphere after vermicompost application. To better understand the impact of vermicompost treatments on the assembly of rhizosphere bacterial communities, 16S rDNA communities of vermicompost and rhizospheres of each peat- and soil-grown tomatoes were profiled after conventional fertigation, irrigation without additional nutrients, and addition of three different vermicompost-extracts. The full dataset consisted of 412 identified genera, of which 317 remained following stringent quality filtration. Tomato rhizosphere microbiome responses to treatments were complex and unique between peat and soil growth substrates. Direct colonization of vermicompost-origin taxa into rhizospheres was limited, with genera Photobacterium and Luteimonas colonizing peat rhizospheres, genera Truepera, Phenylobacterium, and Lysinibacillus colonizing soil rhizospheres, and genus Pelagibius appearing in both soil and peat rhizospheres. Further patterns of differential abundance and presence/absence between treatments highlight vermicompost-mediated effects on rhizosphere microbiome assembly as an interplay of rhizosphere medium, direct colonization of vermicompost-origin taxa and vermicompost-induced shifts in the rhizosphere microbial community. This exploratory analysis is intended to provide an initial look at 16S community composition of vermicompost and the effects of vermicompost treatment on the rhizosphere microbiome assembly to highlight interactions of potential merit for subsequent investigations.

Brisket Disease Is Associated with Lower Volatile Fatty Acid Production and Altered Rumen Microbiome in Holstein Heifers.

Brisket disease is heritable but is also associated with non-genetic risk factors and effects of the disease on the rumen microbiome are unknown. Ten Holstein heifers were exposed to the plateau environment for three months and divided into two groups according to the index of brisket disease, the mean pulmonary arterial pressure (mPAP): brisket disease group (BD, n = 5, mPAP > 63 mmHg) and healthy heifer group (HH, n = 5, mPAP < 41 mmHg). Rumen fluid was collected for analysis of the concentrations of volatile fatty acids (VFAs). Extracted DNA from rumen contents was analyzed using Illumina MiSeq 16S rRNA sequencing technology. The concentration of total VFA and alpha-diversity metrics were significantly lower in BD group (p < 0.05). Ruminococcus and Treponema were significantly decreased in BD heifers (p < 0.05). Correlation analysis indicated that 10 genera were related to the mPAP (p < 0.05). Genera of Anaerofustis, Campylobacter, and Catonella were negatively correlated with total VFA and acetic acid (R < -0.7, p < 0.05), while genera of Blautia, YRC22, Ruminococcus, and Treponema were positively related to total VFA and acetic acid (R > 0.7; p < 0.05). Our findings may be a useful biomarker in future brisket disease work.

Evaluation of warm season annual forages for forage yield and quality in the north-central United States.

Grazing-based dairy operations require productive, high-quality forages capable of supporting the nutritional needs of mid-lactation dairy cows. Our objectives were to evaluate primary and regrowth harvests of two cultivars of sudangrass (SU), sorghum-sudangrass (S×SU), and pearl millet (PM) forages for growth and nutritive characteristics within the specific context of suitability for grazing by dairy cows. Three harvest cycles, including primary and regrowth cycles in 2016, and a single harvest cycle of primary growth in 2017, were evaluated at two locations (Prairie du Sac and Marshfield, WI). Within each cycle, sampling was initiated when canopy height was about 41 cm and continued thereafter on weekly intervals for 5 weeks, resulting in six equally spaced sampling dates per harvest cycle. Data were analyzed as a split-plot design with cultivars (6) as whole-plots arranged in randomized complete blocks and weekly harvest dates (6) as subplots. Yields of dry matter (DM) were less consistent at the more northern location (Marshfield), which is known for its heavier, poorly drained soils. Despite locational differences, the taller-growing cultivar within each forage type frequently exhibited yield advantages over dwarf or shorter-growing cultivars; this occurred for 7 of 9 intra-forage-type comparisons (P ≤ 0.021) across three harvest cycles at Prairie du Sac, and for 6 of 9 similar comparisons (P ≤ 0.032) at Marshfield. In 2016, shorter-growing cultivars had greater percentages of leaf in 4 of 6 intra-forage-type comparisons at both locations (P ≤ 0.004), which is especially relevant for grazing. Similarly, PM cultivars exhibited shorter canopy heights (P ≤ 0.002), but greater percentages of leaf (P < 0.001), than all other cultivars during all harvest cycles at both locations. However, the greater leaf percentages exhibited by PM cultivars did not translate into reduced percentages of structural plant fiber (asNDFom) on a whole-plant basis during any harvest cycle at either location; furthermore, asNDFom concentrations for PM cultivars were greater (P ≤ 0.047) than observed for other cultivars within 3 of 6 harvest cycles across both locations. Ruminal in-situ degradation of asNDFom for whole-plant forages based on a 48-h incubation was significantly greater (P ≤ 0.006) for PM compared with other cultivars in 4 of 6 harvest cycles. Pearl millet cultivars generally exhibited more suitable characteristics for grazing livestock than SU or S×SU cultivars.

Comparison of Protein Precipitation Ability of Structurally Diverse Procyanidin-Rich Condensed Tannins in Two Buffer Systems.

The protein precipitation (PP) of bovine serum albumin (BSA), lysozyme (LYS), and alfalfa leaf protein (ALF) by four procyanidin-rich condensed tannin (CT) samples in both 2-[N-morpholino]ethanesulfonic acid (MES) and a modified Goering-Van Soest (GVS) buffer is described. Purified CT samples examined included Vitis vinifera seed (mean degree of polymerization [mDP] 4.1, 16.5% galloylated), Tilia sp. flowers (B-type linkages, mDP 5.9), Vaccinium macrocarpon berries (mDP 8.7, 31.7% A-type linkages). and Trifolium pratense flowers (B-type linkages, mDP 12.3) and were characterized by 2D NMR (>90% purity). In general, CTs precipitated ALF > LYS ≥ BSA. PP in GVS buffer was 1 to 2.25 times greater than that in MES buffer (25 °C). The GVS buffer system better reflects the results/conclusions from the literature on the impacts mDP, galloylation, and A-type linkages have on PP. Determinations of PP using the MES buffer at 37 °C indicated that some of these differences may be attributed to the temperature at which GVS buffer determinations are conducted. In vitro PP studies using the GVS buffer may offer better guidance when selecting CT-containing forages and amendments for ruminant feeding studies.

Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation.

We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

Vineyard under-vine floor management alters soil microbial composition, while the fruit microbiome shows no corresponding shifts.

The microbiome of a vineyard may play a critical role in fruit development, and consequently, may impact quality properties of grape and wine. Vineyard management approaches that have directly manipulated the microbiome of grape clusters have been studied, but little is known about how vineyard management practices that impact the soil microbial pool can influence this dynamic. We examined three under-vine soil management practices: 1) herbicide application, 2) soil cultivation (vegetation removal), and 3) natural vegetation (no vegetation removal) in a Riesling vineyard in New York over a three-year period. The microbiomes associated with soil and grapes were profiled using high-throughput sequencing of the bacterial 16 S rRNA gene and fungal ITS regions. Our results showed that soil bacterial composition under natural vegetation differs from that seen in glyphosate-maintained bare soil. Soil fungal composition under the natural vegetation treatment was distinct from other treatments. Although our study revealed soil microbiome shifts based on under-vine management, there were no corresponding changes in fruit-associated microbial composition. These results suggested that other vineyard management practices or environmental factors are more influential in shaping the grape-associated microbiome.

Genome Surfing As Driver of Microbial Genomic Diversity.

Historical changes in population size, such as those caused by demographic range expansions, can produce nonadaptive changes in genomic diversity through mechanisms such as gene surfing. We propose that demographic range expansion of a microbial population capable of horizontal gene exchange can result in genome surfing, a mechanism that can cause widespread increase in the pan-genome frequency of genes acquired by horizontal gene exchange. We explain that patterns of genetic diversity within Streptomyces are consistent with genome surfing, and we describe several predictions for testing this hypothesis both in Streptomyces and in other microorganisms.

Selection on soil microbiomes reveals reproducible impacts on plant function.

Soil microorganisms found in the root zone impact plant growth and development, but the potential to harness these benefits is hampered by the sheer abundance and diversity of the players influencing desirable plant traits. Here, we report a high level of reproducibility of soil microbiomes in altering plant flowering time and soil functions when partnered within and between plant hosts. We used a multi-generation experimental system using Arabidopsis thaliana Col to select for soil microbiomes inducing earlier or later flowering times of their hosts. We then inoculated the selected microbiomes from the tenth generation of plantings into the soils of three additional A. thaliana genotypes (Ler, Be, RLD) and a related crucifer (Brassica rapa). With the exception of Ler, all other plant hosts showed a shift in flowering time corresponding with the inoculation of early- or late-flowering microbiomes. Analysis of the soil microbial community using 16 S rRNA gene sequencing showed distinct microbiota profiles assembling by flowering time treatment. Plant hosts grown with the late-flowering-associated microbiomes showed consequent increases in inflorescence biomass for three A. thaliana genotypes and an increase in total biomass for B. rapa. The increase in biomass was correlated with two- to five-fold enhancement of microbial extracellular enzyme activities associated with nitrogen mineralization in soils. The reproducibility of the flowering phenotype across plant hosts suggests that microbiomes can be selected to modify plant traits and coordinate changes in soil resource pools.