Bacteriophages of soil bacilli: A new multivalent phage of Bacillus altitudinis

Mahmud, Rashed; Гарифулина, К И; Ulyanova, Vera; Evtugyn, Vladimir G.; Mindubaeva, L; Хазиева, Л Р; Dudkina, Elena; Vershinina, Valentina; Kolpakov, A. I.; Ilinskaya, О. N.

doi:10.3103/s0891416817020082

Cited by 5 publications

(4 citation statements)

References 27 publications

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“…2, right panel). Andromedaviruses (length range, 47,888 to 48,100 bp) were found in all successional stages at 18, 42, and 49.5 h after wetting and have previously been shown to infect Bacillus hosts (33). Combined, these UViG data indicated that Firmicutes were predominant targets, particularly at the end of the wetting experiment, which led us to further explore this putative link.…”

Section: Resultsmentioning

confidence: 72%

“…The longest circular UViGs belonged to three identical Spbetavirus phages (163,801 bp), which are Siphoviridae phages known to infect soil Bacillus (33). These UViGs were reconstructed independently biocrust metagenomes seen in the early, late-middle (late-mid), and late successional stages, while the early-middle (early-mid) metagenome also contained a smaller Spbetavirus contig of 137,161 bp.…”

Section: Resultsmentioning

confidence: 99%

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Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

Goethem

Swenson

Trubl

et al. 2019

mBio

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Biological soil crusts (biocrusts) are photosynthetic “hot spots” in deserts and cover ∼12% of the Earth’s terrestrial surface, and yet they face an uncertain future given expected shifts in rainfall events. Laboratory wetting of biocrust communities is known to cause a bloom of Firmicutes which rapidly become dominant community members within 2 days after emerging from a sporulated state. We hypothesized that their bacteriophages (phages) would respond to such a dramatic increase in their host’s abundance. In our experiment, wetting caused Firmicutes to bloom and triggered a significant depletion of cyanobacterial diversity. We used genome-resolved metagenomics to link phage to their hosts and found that the bloom of the genus Bacillus correlated with a dramatic increase in the number of Caudovirales phages targeting these diverse spore-formers (r = 0.762). After 2 days, we observed dramatic reductions in the relative abundances of Bacillus, while the number of Bacillus phages continued to increase, suggestive of a predator-prey relationship. We found predicted auxiliary metabolic genes (AMGs) associated with sporulation in several Caudovirales genomes, suggesting that phages may influence and even benefit from sporulation dynamics in biocrusts. Prophage elements and CRISPR-Cas repeats in Firmicutes metagenome-assembled genomes (MAGs) provide evidence of recent infection events by phages, which were corroborated by mapping viral contigs to their host MAGs. Combined, these findings suggest that the blooming Firmicutes become primary targets for biocrust Caudovirales phages, consistent with the classical “kill-the-winner” hypothesis. IMPORTANCE This work forms part of an overarching research theme studying the effects of a changing climate on biological soil crust (biocrust) in the Southwestern United States. To our knowledge, this study was the first to characterize bacteriophages in biocrust and offers a view into the ecology of phages in response to a laboratory wetting experiment. The phages identified here represent lineages of Caudovirales, and we found that the dynamics of their interactions with their Firmicutes hosts explain the collapse of a bacterial bloom that was induced by wetting. Moreover, we show that phages carried host-altering metabolic genes and found evidence of proviral infection and CRISPR-Cas repeats within host genomes. Our results suggest that phages exert controls on population density by lysing dominant bacterial hosts and that they further impact biocrust by acquiring host genes for sporulation. Future research should explore how dominant these phages are in other biocrust communities and quantify how much the control and lysis of blooming populations contributes to nutrient cycling in biocrusts.

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Section: Resultsmentioning

confidence: 72%

Section: Resultsmentioning

confidence: 99%

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

Goethem

Swenson

Trubl

et al. 2019

mBio

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“…In the function prediction of soil fungi, it was found that the relative abundance of saprophytes accounted for the majority in all treatments. Such organisms feed on dead organic matter and can decompose dead and weakened organic matter into simple substances for easy absorption and recycling by plants, which is beneficial to soil nutrient activation and crop growth and extremely important to soil ecosystems ( Mahmud et al, 2017 ). In addition, it was found that the soil fungal communities exhibited the special functions of plant endophytes, plant saprophytes, and wood saprophytes due to the application of different botanical oil meals.…”

Section: Discussionmentioning

confidence: 99%

Effects of different botanical oil meal mixed with cow manure organic fertilizers on soil microbial community and function and tobacco yield and quality

Chen

Qin³

et al. 2023

Front. Microbiol.

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IntroductionThe continuous application of cow manure in soil for many years leads to the accumulation of heavy metals, pathogenic microorganisms, and antibiotic resistance genes. Therefore, in recent years, cow manure has often been mixed with botanical oil meal as organic fertilizer applied to farmland to improve soil and crop quality. However, the effects of various botanical oil meal and cow manure mixed organic fertilizers on soil microbial composition, community structure, and function, tobacco yield, and quality remain unclear.MethodsTherefore, we prepared organic manure via solid fermentation by mixing cow manure with different oil meals (soybean meal, rape meal, peanut bran, sesame meal). Then, we studied its effects on soil microbial community structure and function, physicochemical properties, enzyme activities, tobacco yield and quality; then we analyzed the correlations between these factors.Results and discussionCompared with cow manure alone, the four kinds of mixed botanical oil meal and cow manure improved the yield and quality of flue-cured tobacco to different degrees. Peanut bran, which significantly improved the soil available phosphorus, available potassium, and NO3–-N, was the best addition. Compared with cow manure alone, soil fungal diversity was significantly decreased when rape meal or peanut bran was combined with cow manure, while soil bacterial and fungal abundance was significantly increased when rape meal was added compared with soybean meal or peanut bran. The addition of different botanical oil meals significantly enriched the subgroup_7 and Spingomonas bacteria and Chaetomium and Penicillium fungi in the soil. The relative abundances of functional genes of xenobiotics biodegradation and metabolism, soil endophytic fungi, and wood saprotroph functional groups increased. In addition, alkaline phosphatase had the greatest effect on soil microorganisms, while NO3–-N had the least effect on soil microorganisms. In conclusion, the mixed application of cow manure and botanical oil meal increased the available phosphorus and potassium contents in soil; enriched beneficial microorganisms; promoted the metabolic function of soil microorganisms; increased the yield and quality of tobacco; and improved the soil microecology.

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“…Phagotyping methods are used to distinguish Salmonella, including the most common in Poland serotype Salmonella Enteritidis [Dera-Tomaszewska and Tokarska-Pietrzak 2012]. Phagotyping is also used to identify soil bacteria of the genus Bacillus that can be a source of food contamination [Shah Mahmud et al 2017].…”

Section: Phagotyping Methodsmentioning

confidence: 99%

Methods in food science and technology. Part 1

Walczycka¹,

Błaszczyk²

2022

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We would like to present to you a monograph entitled "Methods in food science and technology -part 1", which we hope will be warmly accepted and continued. Our intention was to gather in one place descriptions of modern methods used in science related to food and human nutrition. Although the monograph is written in English, it has been prepared in such a way that it can be used in the didactic process by teachers and their students and doctoral students. Each chapter is a separate whole, i.e. it is devoted to a different method or group of methods or techniques for food analysis, both in terms of its chemical composition, physical properties, sensory qualities, as well as its quality, stability and safety. The aim of the monograph is to present terminology and specialist vocabulary in an accessible way for a reader who is not a specialist in a given discipline. Importantly, individual chapters have been reviewed by at least two experts. We wish you pleasant reading and fruitful use of the monograph.

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Bacteriophages of soil bacilli: A new multivalent phage of Bacillus altitudinis

Cited by 5 publications

References 27 publications

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

Characteristics of Wetting-Induced Bacteriophage Blooms in Biological Soil Crust

Effects of different botanical oil meal mixed with cow manure organic fertilizers on soil microbial community and function and tobacco yield and quality

Methods in food science and technology. Part 1

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