910 metagenome-assembled genomes from the phytobiomes of three urban-farmed leafy Asian greens

Abstract

The genome sequences of many microbial species from the phytobiomes of several leafy Asian greens remain unknown. Here, we address this gap by reconstructing 910 prokaryotic draft genomes from 24 leaf, 65 root, 12 soil, and 6 compost metagenomes from the seedling and adult developmental stages of three leafy Asian greens-Brassica rapa var. parachinensis, Brassica oleracea var. alboglabra and Amaranthus spp.-grown in a commercial, soil-based urban farm. Of these, 128 are near-complete (>90% completeness, <5% redundancy), 540 are substantially complete (≥70% completeness, <10%, redundancy), while the rest have a completeness ≥50% and redundancy <10%. The draft genomes together span 292 bacterial and 3 archaeal species, a subset of which are from underrepresented genuslevel lineages in public databases. We expect our dataset to facilitate a wide range of comparative studies that seek to understand the different functional aspects of vegetable crop phytobiomes and for devising new strategies for microbial cultivation in the future. Background & Summary Microbiomes within the phytobiome 1-the plant, its environment, and its associated communities of organisms-affect nearly all aspects of growth such as development, differentiation, nutrient acquisition, and tolerance to biotic and abiotic stresses 2. Previous studies have greatly expanded our understanding of the diversity and composition of specific phytobiome-associated microbiomes 3-9 , but only a few have investigated their genetic underpinnings in a systematic manner 10,11. Knowledge of the latter is especially critical for improving our ability to manipulate phytobiome-associated microbiomes with a view to enhance crop productivity and agricultural sustainability. Metagenomic strategies used to gain such insights rely on curated and well-referenced catalogs of microbial reference genomes that have been specifically recovered from phytobiome-associated microbiomes. Using a catalog of 3,837 bacterial reference genomes, 1,160 of which were from a limited number of phytobiomes, Levy et al. 10 identified genetic traits associated with bacterial adaptation to the phytobiome. Deeper insights into other aspects such as identifying the functional roles of different microbial species within the phytobiomes of specific crops will, however, require access to an expanded catalog of microbial reference genomes recovered from crop phytobiomes of interest. Leafy Asian greens which include a range of Brassicas and Amaranthus are widely consumed in Asia and are rich in phytochemicals with known health benefits 12. They are well suited for cultivation in urban farms 13 , where microbiome-based solutions can be readily test-bedded in comparison to trials in large, conventional agricultural farms. Although leafy Brassicas represent the nearest commercial crops to the model plant Arabidopsis, their microbiomes remain poorly understood in comparison to the latter. Similarly, the microbiomes of low-cost leafy vegetables such as Amaranthus, also remain poorly understood.

Enabling sustainable agriculture through understanding and enhancement of microbiomes

“…The vast majority of genome‐resolved metagenomics have produced uncurated draft genomes (i.e. metagenome‐assembled genomes (MAGs) (Zhang et al ., 2017; Bandla et al ., 2020)), but gaps, assembly errors and contamination from other genomes limit the utility of these assembled genomes to general genomic studies (L. X. Chen et al ., 2020). Recent advanced genome curation techniques allow generation of complete (circularized, no gap) MAGs (cMAGs) from very complex microbial communities including soil and sediments (L. X. Chen et al ., 2020).…”

Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions

“…We checked for the presence of our 60 MAGs in two publicly available MAG datasets [ 22 , 23 ]. The recovery of the “same” genome from different environments lends additional confidence to our MAG recovery process.…”

“…The recovery of the “same” genome from different environments lends additional confidence to our MAG recovery process. Among the 910 MAGs from the Asian soil, plant-based compost, and leafy greens phytobiomes [ 23 ] we found no relevant hits (i.e., ANI was less than 85%). We did find hits (ANI ≥ 95%) for 30 of our ZC3/ZC4 60 MAGs in the Genomes from the Earth’s Microbiomes (GEM) catalog [ 22 ] (Fig.…”

“…Shotgun metagenomic sequencing has helped to reveal the diversity of microbial communities in natural habitats [ 15 ] and in engineered environments such as composting [ 1 , 16 ] or sludge digesters [ 17 ]. New methods and computational tools now allow the recovery of metagenome-assembled genomes (MAGs) from complex ecosystems [ 18 – 23 ]. The study of MAGs from microorganisms in a given environment can provide detailed taxonomical and functional diversity information, and therefore has the potential to allow a better understanding of their ecological context and metabolic arsenal [ 22 , 24 ].…”

Oil Palm Fatal Yellowing (FY), a Disease with an Elusive Causal Agent

“…This type of methodology allows, in addition to identifying microorganisms present, access to their genomes. This creates the possibility of studying the genetic relationship among the species present, and predicting metabolic capabilities as well as the interactions between the organisms of the community [97]. One limitation to this method, however, is that the plant host genome sequence needs to be available and subtracted in silico from microbial community sequences.…”