Root microbiome response to treated wastewater irrigation

Zolti, Avihai; Green, Stefan J.; Mordechay, Evyatar Ben; Hadar, Yitzhak; Minz, Dror

doi:10.1016/j.scitotenv.2018.11.251

Cited by 74 publications

(59 citation statements)

References 48 publications

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“…We previously measured significant increases in pH, dissolved organic matter (DOC) and electrical conductivity (EC) in TWW-irrigated soils relative to FW-irrigated soils (26)(also at Table S6 ). Similar patterns were observed in this study through canonical correspondence analysis (CCA) ( Figure 2e ).…”

Section: Resultsmentioning

confidence: 99%

“…All samples were composites, consisting of 2-4 plants collected from separate lysimeters, except for FW irrigated lettuce plants which were collected from two lysimeters and were composites of 2 plants each. Detailed procedures, including soil and plant measurements, were described previously (26).…”

Section: Methodsmentioning

confidence: 99%

“…Standard phenol-chloroform nucleic acid extraction protocol was employed for DNA and RNA isolation (26, 73). In brief, 0.2 gr of roots were moderately bead beaten for 45 s at low speed (4.5 m/s) by Fast Prep FP120 (Savant Instruments Inc., Holbrook, NY, USA) with phenol, phosphate buffer pH 8 (with additional 10 μl ml−1 β-mercaptoethanol -Sigma-Aldrich, St Louis, MO, USA) and 1.25% CTAB (Hexadecyltrimethylammonium bromide, Sigma Aldrich).…”

Section: Methodsmentioning

confidence: 99%

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The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

Zolti

Green

Sela

et al. 2019

Preprint

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Microbial communities are highly responsive to environmental cues, and both their structure and activity can be altered in response to changing conditions. We hypothesized that host-associated microbial communities, particularly those colonizing host surfaces, can serve as in situ sensors to reveal environmental conditions experienced by both microorganisms and the host. For a proof-of-concept, we studied a model plant-soil system and employed a non-deterministic gene-centric approach. A holistic analysis was performed using plants of two species and irrigation with water of low quality to induce host stress. Our analyses examined the genetic potential (DNA) and gene expression patterns (RNA) of plant-associated microbial communities, as well as transcriptional profiling of host plants. Transcriptional analysis of plants irrigated with treated wastewater revealed significant enrichment of general stress-associated root transcripts relative to plants irrigated with fresh water. Metagenomic analysis of root-associated microbial communities in treated wastewater-irrigated plants, however, revealed enrichment of more specific stress-associated genes relating to high levels of salt, high pH and lower levels of oxygen. Meta-analysis of these differentially abundant genes obtained from other metagenome studies provided evidence of the link between environmental factors such as pH and oxygen and these genes. Analysis of microbial transcriptional response demonstrated that enriched gene content was actively expressed, which implies contemporary response to elevated levels of pH and salt. We demonstrate here that microbial profiling can elucidate stress signals that cannot be observed even through interrogation of host transcriptome, leading to an alternate mechanism for evaluating in situ conditions experienced by host organisms.Significance StatementThis study examines the potential for microbial communities to provide insight into stresses experienced by their eukaryotic host organisms, through profiling of metagenomes and metatranscriptomes. Our study uses plant host-associated microorganisms as an in vivo and in situ microsensor to identify environmental stresses experienced by the microbial community and by the plant. Transcriptionally active host-associated microbial communities are responsive in a highly specific manner to environmental conditions. Conversely, host transcriptome sequencing provides only a very general stress response. This study is a proof-of-concept for the use of microbial communities as microsensors, with a great potential for interrogation of a wide range of host systems.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

Zolti

Green

Sela

et al. 2019

Preprint

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“…Many scholars use this technique to detect the soil environment. Effects of root exudates on soil microorganisms have been partially reported [9][10]. However, it is mainly concentrated in field crops or plants in the original ecological environment [11], and there is still a lack of targeted studies on the effects of garlic rotation on soil microbial community of facility continuous cropping.…”

Section: Introductionmentioning

confidence: 99%

Effects of Garlic Rotation and Organic Fertilizer Application on Bacterial Community Structure in Rhizosphere Soil of Continuous Cropping Tomato

Zhao¹,

Yin²,

Song³

et al. 2020

Journal of Bio-agriculture

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16S/18S/ITS's amplicon and metagenome sequencing had been used extensively to investigate the root mi- crobial community structure of crops and model plants. In this study, the rhizosphere soils of the continuous cropping (Control), garlic rotation and organic fertilizer application tomato plants were taken as the test samples, respectively, to measure the microbial community structure and soil enzyme activities. The results showed that both planting modes had significant effects on the microecology of continuous cropping tomato rhizosphere soil. After garlic rotation, the diversity (Shannon index and Simpson index) and relative abundance (Ace index and Chao1 index) of soil bacterial community decreased significantly in the early stage, but increased significantly in the later stage. These changes could be significantly alleviated by the application of organic fertilizer. During the whole growth period of tomato plants, the activities the six soil enzymes (sucrase, catalase, urease, protease, amylase and alkaline phosphatase) were all the highest in the organic fertilizer application plot, followed by the rotation plot and the continuous cropping plot. With the extension of planting time, the activities of soil protease, urease and alkaline phosphatase increased gradually, while that of sucrase decreased gradually. Catalase activity initially increased and then decreased, while amylase activity did not change significantly with time. After garlic rotation, mortality rate of tomato plants decreased significantly, and all growth indexes were significantly better than those of the control treatment. To sum up, garlic/tomato rotation can effectively improve the soil environment and alleviate the continuous cropping obstacle of tomatoes in greenhouse. Moreover, rotation combining with organic fertilizer application can acquire the most obvious mitigation effect.

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“…present a conceptual description of the pipeline applied in this study.Amplicon sequencing, shotgun metagenomic and meta-transcriptomics analyses Tomato soil and root samples and lettuce root samples were collected as previously described(63). Briefly, tomato (Solanum lycopersicum-Heinz 4107) and lettuce (Lactuca sativa-Romaine-Assaph) seedling were planted and grown for 42 days in a random block lysimeters experiment, at Lachish agricultural research station in Kiryat-Gat, Israel.…”

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confidence: 99%

Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome

Dror

Wang

Jurkevitch

et al. 2020

Preprint

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20Polyketides (PK) and nonribosomal peptides (NRP) are two microbial secondary metabolite 21 (SM) families largely known for their variety of functions, including antimicrobials, 22 siderophores and others. Despite their involvement in bacteria-bacteria and bacteria-plant 23 interactions, root-associated SM are largely unexplored due to the limited cultivability of 24 bacteria. Here, we analyzed the diversity, composition and expression of SM-encoding 25 biosynthetic gene clusters (BGC) in root microbiomes by culture-independent amplicon 26 sequencing, shotgun metagenomics and metatranscriptomics. Roots (tomato and lettuce) 27 harbored distinct compositions of nonribosomal peptide synthetases (NRPS) and polyketide 28 synthases (PKS) relative to the adjacent bulk soil, and specific BGCs were both enriched and 29 highly expressed in the root microbiomes. While several of the highly abundant and expressed 30 sequences were remotely associated with BGCs encoding antimicrobials, the low similarity to 31 characterized genes suggests their potential novelty. A subset of these genes were screened 32 against a large set of soil-derived cosmid libraries, from which five whole NRPS/PKS BGCs of 33 unknown function were retrieved. Three clusters were taxonomically affiliated with 34 Actinobacteria, while the remaining two were associated with hosts of unknown phylogeny. One 35Streptomyces-derived BGC was predicted to encode for a polyene with potential antifungal 36 activity, while the others were too novel to predict. Screening against a suite of metagenomic 37 datasets revealed that all clusters were profuse in soil and roots, and almost completely absent in 38 aquatic and gut environments, supporting the notion that they play a specific role in root 39 ecosystems. Overall, our results indicate that root microbiomes harbor a specific assemblage of 40 yet undiscovered SM.41 42 3 43 Importance 44 We identified distinct secondary metabolite (polyketide and nonribosomal peptide) encoding 45 genes that are enriched (relative to adjacent bulk soil) and expressed in root ecosystems, yet 46 almost completely absent in human gut and aquatic environments. Several of the genes were 47 distantly related to genes encoding for antimicrobials and siderophores, although the high 48 sequence variability suggests that they encode for novel metabolites and may have unique 49 ecological functions. This study demonstrates that plant roots harbor a diverse array of unique 50 secondary metabolite encoding genes that are highly enriched and expressed in the root 51 ecosystem. The secondary metabolites encoded by these genes are undoubtedly required for 52 bacterial colonization and persistence in the root environment and are most likely associated with 53 inter-bacterial and bacterial-plant interactions. 54 55 Keywords: Soil microbiome, root microbiome, polyketides, nonribosomal peptides, secondary 56 metabolites, plant-microbe interactions 57 58 59 60 61 62 63 64Soil is an extremely diverse ecosystem that contains a myriad of micro-and macr...

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Root microbiome response to treated wastewater irrigation

Cited by 74 publications

References 48 publications

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts

Effects of Garlic Rotation and Organic Fertilizer Application on Bacterial Community Structure in Rhizosphere Soil of Continuous Cropping Tomato

Elucidating the diversity and potential function of nonribosomal peptide and polyketide biosynthetic gene clusters in the root microbiome

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