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.

Peatlands are both responding to and influencing climate change. While numerous studies on peatland carbon dynamics have been published in boreal and temperate regions for decades, a much smaller yet growing body of scientific articles related to tropical peatlands has recently been published, including from previously overlooked regions such as the Amazonian and Congo basins. The recent recognition of tropical peatlands as valuable ecosystems because of the organic carbon they accumulate in their water-saturated soils has occurred after most of them have been drained and degraded in Southeast Asia. Under disturbed conditions, their natural carbon storage function is shifted to an additional carbon source to the atmosphere. Understanding the effect of land-use change and management practices on peatlands can shed light on the driving variables that influence carbon emissions and can model the magnitude of emissions in future degraded peatlands. This is of primary importance as other peatland-covered regions in the tropics are at risk of land-use and land-cover changes. A systematic review that synthesizes the general understanding of tropical peatland carbon dynamics based on the published literature is much needed to guide future research directions on this topic. Moreover, previous studies of biogeochemical cycling in tropical peatlands have largely focused on terrestrial stocks and fluxes with little attention given to document lateral and downstream aquatic export through natural and artificial drainage channels. Here, we present a systematic review protocol to describe terrestrial and aquatic carbon dynamics in tropical peatlands and identify the influence of land-use change on carbon exchange. We described a set of literature search and screening steps that lay the groundwork for a future synthesis on tropical peatlands carbon cycling. Such an evidence-based synthesis using a systematic review approach will help provide the research community and policymakers with consistent science-based guidelines to set and monitor emissions reduction targets as part of the forestry and land-use sector.

We report five canine rabies virus genome sequences from India that were obtained from brain samples using Oxford Nanopore Technologies sequencing. The sequences will facilitate understanding of the evolution and transmission of rabies.

Tropical peatlands in South-East Asia are some of the most carbon-dense ecosystems in the world. Extensive repurposing of such peatlands for forestry and agriculture has resulted in substantial microbially-driven carbon emissions. However, we lack an understanding of the microorganisms and their metabolic pathways involved in carbon turnover. Here, we address this gap by reconstructing 764 sub-species-level genomes from peat microbiomes sampled from an oil palm plantation located on a peatland in Indonesia. The 764 genomes cluster into 333 microbial species (245 bacterial and 88 archaeal), of which, 47 are near-complete (completeness ≥90%, redundancy ≤5%, number of unique tRNAs ≥18) and 170 are substantially complete (completeness ≥70%, redundancy ≤10%). The capacity to respire amino acids, fatty acids, and polysaccharides was widespread in both bacterial and archaeal genomes. In contrast, the ability to sequester carbon was detected only in a few bacterial genomes. We expect our collection of reference genomes to help fill some of the existing knowledge gaps about microbial diversity and carbon metabolism in tropical peatlands.