Microorganisms are critically important for the function of surface water ecosystems but are frequently subjected to anthropogenic disturbances at either acute (pulse) or long-term (press) scales. Response and recovery of microbial community composition and function following pulse disturbance is well-studied in controlled, laboratory scale experiments but is less well-understood in natural environments undergoing continual press disturbance. The objectives of this study were to determine the drivers of sediment microbial compositional and functional changes in freshwaters receiving continual press disturbance from agricultural land runoff and to evaluate the ability of the native microbial community to resist disturbance related changes as a proxy for freshwater ecosystem health. Freshwater sediments were collected seasonally over 1 year in Kewaunee County, Wisconsin, a region impacted by concentrated dairy cattle farming, manure fertilization, and associated agricultural runoff which together serve as a press disturbance. Using 16S rRNA gene amplicon sequencing, we found that sediments in locations strongly impacted by intensive agriculture contain significantly higher abundances ( p < 0.01) of the genera Thiobacillus, Methylotenera, Crenotrhix, Nitrospira , and Rhodoferax compared to reference sediments, and functions including nitrate reduction, nitrite reduction, and nitrogen respiration are significantly higher ( p < 0.05) at locations in close proximity to large farms. Nine species-level potential human pathogens were identified in riverine sediments including Acinetobacer lwoffi and Arcobacter skirrowii , two pathogens associated with the cattle microbiome. Microbial community composition at locations in close proximity to intensive agriculture was not resistant nor resilient to agricultural runoff disturbance within 5 months post-disturbance but did reach a new, stable microbial composition. From this data, we conclude that sediment microbial community composition is sensitive and shifts in response to chemical and microbial pollution from intensive agriculture, has a low capacity to resist infiltration by non-native, harmful bacteria and, overall, the natural buffering capacity of freshwater ecosystems is unable to fully resist the impacts from agricultural press disturbance.

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.

&lt;p&gt;Over the past few decades, tropical peatlands in Southeast Asia have been heavily degraded for multiple land uses, mainly by employing drainage and fire. More importantly, the extent of these degraded areas, primarily covered with ferns and sedges, have increased to almost 10% of the total peatland area in Southeast Asia. In particular, the role of sedges in plant-mediated gas transport to the atmosphere has been recognized as a significant CH&lt;sub&gt;4&lt;/sub&gt; pathway in northern peatlands, however, in the Tropics this is still unknown. Within this context, we adopted an integrated approach using on-site measurements (CH&lt;sub&gt;4&lt;/sub&gt;, porewater physicochemical characteristics) with genomics to investigate the role of hydrology, vegetation structure, and microbiome on CH&lt;sub&gt;4&lt;/sub&gt; emission from fire-degraded tropical peatland in Brunei.&lt;/p&gt;&lt;p&gt;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160; We found for the first time that in degraded tropical peatlands of Southeast Asia, sedges transported 70-80% of the total CH&lt;sub&gt;4&lt;/sub&gt; emission and significantly varied with values ranging from 1.22&amp;#177;0.13 to 6.15&amp;#177;0.57 mg CH&lt;sub&gt;4&lt;/sub&gt; m&lt;sup&gt;-2&lt;/sup&gt; hr&lt;sup&gt;-1&lt;/sup&gt;, during dry and wet period, respectively. This variation was mainly attributed to water table position along with changes in sedge cover and porewater properties, which created more optimal methanogenesis conditions. Total emissions via this process might increase in the future as the extent of degraded tropical peatlands expands due to more frequent fire episodes and flooding.&lt;/p&gt;&lt;p&gt;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160;&amp;#160; Further, we used 16S rRNA high-throughput sequencing to investigate the microbiomes in peat profile (above and below water table) as well as rhizo-compartments (Rhizosphere, Rhizoplane, Endosphere) of sedges. We found that the peat profile as well as rhizo-compartments of sedge harboured a higher number of methanogenic archaea in the order Methanomicrobiales and Methanobacteriales, compared to non-burnt and bulk soil, which further explains our findings of higher CH&lt;sub&gt;4&lt;/sub&gt; emission from degraded tropical peatland areas covered with sedges. These insights into the impact of fire on hydrology, vegetation structure, and microbial community composition on CH&lt;sub&gt;4&lt;/sub&gt; emissions provide an important basis for future studies on CH&lt;sub&gt;4&lt;/sub&gt; dynamics in degraded tropical peatland areas.&lt;/p&gt;