Jonathan M Adams

Jonathan M Adams
Nanjing University | NJU · School of Geographic and Oceanographic Sciences

PhD in Quaternary Geology, University of Aix-Marseille II, France
Exploring microbial ecology using DNA from the environment

About

263
Publications
66,960
Reads
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8,197
Citations
Introduction
I'm mostly exploring patterns in diversity and community structure of small soil and sediment organisms: bacteria, archaea, fungi and small metazoans, using massively parallel DNA sequencing. If you are interested in doing a postdoc or PhD with me at Nanjing University, and have bioinformatics/microbial ecology experience, please let me know through messaging me on ResearchGate!
Additional affiliations
September 2009 - May 2017
Seoul National University
Position
  • Professor
September 2004 - December 2008
Rutgers, The State University of New Jersey
Position
  • Professor (Assistant)
October 1998 - October 1999
University of Adelaide
Position
  • Lecturer
Education
June 1993 - June 1995
Université de la Mediterranee Aix-Marseille II
Field of study
  • Quaternary Geology
September 1987 - November 1988
Bangor University
Field of study
  • Ecology
October 1983 - June 1986
University of Oxford
Field of study
  • Botany

Publications

Publications (263)
Article
Full-text available
The beneficial effect of crop residue amendment on soil organic carbon (SOC) stock and stability depends on the functional response of soil microbial communities. Here we synchronized microbial metagenomic analysis, nuclear magnetic resonance and plant- ¹⁵ N labeling technologies to gain understanding of how microbial metabolic processes affect SOC...
Article
The extent to which propagule limitation can govern the responses of microbially-mediated processes (such as methane oxidation) to sudden environmental changes, is poorly understood. Here, we compared the ability of the methanotroph community in lakeshore soils of two lakes to respond to an experimental increase in salinity. One set of samples was...
Article
The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co‐occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in...
Article
Plant nitrogen (N) acquisition is essential to both crop growth and yield. A rational N management strategy for agricultural systems under climate change is required but a knowledge gap still exists regarding plant N uptake and N origin (soil-derived N or fertilizer-derived N) in response to elevated atmospheric CO2 and warming. Our study investiga...
Article
Archaeal ammonia oxidizers (AOA) are important in converting ammonia into nitrates in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has been poorly understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogen...
Article
Arbuscular mycorrhizal (AM) fungi play an important role in facilitating ecosystem function and stability. Yet, their community response patterns and ecological assembly processes along elevational gradients which cross a range of climates and soil conditions remain elusive. We used Illumina MiSeq sequencing to examine trends in soil AM fungal comm...
Article
Microbes dominate terrestrial ecosystems via their great species diversity and vital ecosystem functions, such as biogeochemical cycling and mycorrhizal symbiosis. Fungi and other organisms form diverse association networks. However, the roles of species belonging to different kingdoms in multi‐kingdom community networks have remained largely elusi...
Article
Although fairy rings are widely observed, little is known of community processes associated with them. We studied fairy rings in natural grassland in Northern Mongolia, sampling soils outside (‘future’), directly under (‘present’), and within (‘past’) the rings, to represent different time stages during expansion of fairy rings. Soil DNA was extrac...
Article
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There has been little study on the biogeographical patterns of microbial co-occurrence, especially in agricultural soils. Here we investigated the biogeographical patterns and major drivers of co-occurrence network topological structure, and the relative abundance of keystone taxa for soil bacterial and fungal communities using high-throughput sequ...
Article
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In a recent study, we found a distinct soil bacterial community associated with male and female plants of the desert gymnosperm Welwitschia mirabilis. In this subsequent study, we also found that the soil fungal community associated with Welwitschia differs between male and female plants, and between unvegetated areas and the soil under plants. Sit...
Article
Mineral extraction is known to affect soil fungi in polar environments, but it is unknown how long these effects persist. Here, by amplifying the internal transcribed spacer regions of rRNA genes in soil fungi, we compared soil fungal community in intact natural tundra with that in a nearby former coal mining area, abandoned 52 years previously, on...
Article
Nematodes play an important role in ecosystems, yet very little is known about their assembly processes and the factors influencing them. We studied nematode communities in bulk soil from three Asian mountain ecosystems to study the assembly processes of free-living nematode metacommunities and their driving factors. On each mountain, elevations sp...
Article
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The widely used QEN Paleovegetation Atlas has existed for more than 20 years, but its maps were in a simple Jpeg form, not a GIS form. This has limited their use for modelling in biogeography, archaeology and climate modelling. Thanks to funding generously provided by the School of Geography and Oceanography of Nanjing University, the original map...
Article
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Plastics are accumulating in the world’s oceans, while ocean waters are becoming acidified by increased CO2. We compared metagenome of biofilms on tethered plastic bottles in subtidal waters off Japan naturally enriched in CO2, compared to normal ambient CO2 levels. Extending from an earlier amplicon study of bacteria, we used metagenomics to provi...
Preprint
Background: Keystone genes exert great influence on maintaining microbiome stability and functional recovery irrespective of their environmental abundance. Elucidating the effects of environmental stresses on their variation is vital for identifying the recovery potential of ecosystems and regulating microbial adaptation within. Extracellular and i...
Article
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Nematodes play vital roles in soil ecosystems. To understand how their communities and coexistence patterns change along the elevation as well as to determine the best explanatory factors underlying these changes, we investigated free-living soil nematodes on Mt. Halla, South Korea, using an amplicon sequencing approach targeting the 18S rRNA gene....
Article
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Island biogeography theory (IBT) is one of the most fruitful paradigms in macroecology, positing positive species-area and negative species-isolation relationships for the distribution of organisms. Biotic interactions are also crucial for diversity maintenance on islands. In the context of a timberline tree species ( Betula ermanii ) as “virtual i...
Article
Classically, ecologists have considered that biota becomes more integrated and interdependent with ecosystem development in primary successional environments. However, recent work on soil microbial communities suggests that there may in fact be no change in network integration over successional time series. Here, we performed a test of this princip...
Article
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The elevational distributions of bacterial communities in natural mountain forests, especially along large elevational gradients, have been studied for many years. However, the distributional patterns that underlie variations in soil bacterial communities along small-scale elevational gradients in urban ecosystems are not yet well understood. Using...
Article
Aegilops tauschii, the wild progenitor of wheat D-genome and a valuable germplasm for wheat improvement, has a wide natural distribution from eastern Turkey to China. However, the phylogenetic relationship and dispersion history of Ae. tauschii in China has not been scientifically clarified. In this study, we genotyped 208 accessions (with 104 in C...
Preprint
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Edge effects, the altered abiotic and biotic conditions on the borders of natural areas, rarely extend more than a few hundred meters. Edge effects have rarely been linked to altered soil biota, which shape ecosystem processes including carbon storage, biogeochemical cycling, and plant performance. Here, we investigated if agriculturally-mediated i...
Article
Little is known about how bacterial endophyte communities may vary from one tree to another of the same species. We sampled nine standardized replicates from the green stems of an ethnomedicinal tropical tree, Santiria apiculata, in a Malaysian rainforest, to investigate endophyte variation from one plant to another. DNA was extracted axenically fr...
Article
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In the context of global warming, changes in phytoplankton-associated bacterial communities have the potential to change biogeochemical cycling and food webs in marine ecosystems. Skeletonema is a cosmopolitan diatom genus in coastal waters worldwide. Here, we grew a Skeletonema strain with its native bacterial assemblage at different temperatures...
Article
Soil fungi play an important role in promoting nutrient cycling and maintaining ecosystem stability. Yet, there has been little understanding of how fungal co-occurrence networks differ along elevational climate gradients, a topic of interest to both macroecology and climate change studies. Based on high-throughput sequencing technology, we investi...
Article
Empirical studies have intensively clarified the effects of livestock manure on soil fertility, crop yield and microbial community, with little information about their response to application of peanut straw and green manure in dryland of Ultisols. In this study, quantitative polymerase chain reaction (qPCR) and next-generation sequencing were used...
Article
Elevational patterns in taxonomic diversity have been widely studied, but there has been little attention given to patterns in functional gene diversity. We used a metagenomic approach – along with amplicon data - to study trends in functional gene diversity in bacteria along a 2,300 m elevational gradient on Mt. Norikura, Japan. We hypothesized th...
Article
Nutrient resource availability is a crucial environmental factor in determining soil bacterial community assembly. However, the effects of nutrient availability on niche differentiation and temporal co-occurrence patterns of bacterial communities remain elusive. Here, we retrieved sequencing datasets (105 amplicon samples of bacterial 16S rRNA gene...
Preprint
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Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, the trends of co-occurrence networks across similar gradients remain elusive. Here, we constructed co-occurrence networks for fungal community along a 2300 m elevation gradient on Mt Norikura, Japan, hypothesizing a prog...
Article
This study used integrated omics technologies to investigate the potential novel pathways and enzymes for 1,4-dioxane degradation by a consortium enriched from activated sludge of a domestic wastewater treatment plant. An unclassified genus belonging to Xanthobacteraceae increased significantly after magnetic nanoparticle-mediated isolation for 1,4...
Article
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The discovery of complete ammonia oxidation (comammox), oxidizing ammonia to nitrate via nitrite in a single organism, has redefined the traditional recognition of the two-step nitrification driven by two functional groups (ammonia-oxidizing and nitrite-oxidizing microorganisms). However, the understanding of the distribution and niche differentiat...
Article
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Little is known of the earliest stages of soil biota development of volcanic ash, and how rapidly it can proceed. We investigated the potential for soil biota development during the first 3 years, using outdoor mesocosms of sterile, freshly fallen volcanic ash from the Sakurajima volcano, Japan. Mesocosms were positioned in a range of climates acro...
Article
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The effects of ocean acidification on ecosystems remain poorly understood, because it is difficult to simulate the effects of elevated CO2 on entire marine communities. Natural systems enriched in CO2 are being used to help understand the long-term effects of ocean acidification in situ. Here, we compared biofilm bacterial communities on intertidal...
Article
The increasing quantity of plastic waste in the ocean is providing a growing and more widespread novel habitat for microbes. Plastics have taxonomically distinct microbial communities (termed the ‘Plastisphere’) and can raft these unique communities over great distances. In order to understand the Plastisphere properly it will be important to work...
Article
Exotic Spartina alterniflora has become widely distributed along most of the coastlines in China in a wide range of inundation frequencies. However, the assembly processes and co-occurrence patterns of the bacterial community in S. alterniflora wetlands under different inundation frequencies remain elusive. In this study, an in-situ mesocosm was es...
Article
Members of the genus Vibrio are ubiquitous in aquatic environments and can be found either in a culturable or a viable but nonculturable (VBNC) state. Despite widespread concerns as to how to define the occurrence and dynamics of Vibrio populations by culture-independent approaches, further physiological research and relevant biotechnological devel...
Article
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After the discovery of complete ammonia-oxidizing (comammox) Nitrospira, detection and assessments of the contribution of comammox Nitrospira communities to nitrogen cycling are in great demand. PCR-based approach, a common method for the detection of comammox, depends strongly on accurate amplification of the amoA genes from the original DNA sampl...
Article
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Understanding the effects of eutrophication on heterotrophic bacteria, a primary responder to eutrophication, is critical for predicting the responses of ecosystems to marine environmental pollution. Vibrio are indigenous in coastal water and of significance to geochemical cycling and public health. In this study, we investigated the diversity and...
Article
Desert and semi-desert plants are often associated with a distinct soil biota under the plants and close to the root system. We aimed to understand if similar effects could be found in the taxonomically isolated desert gymnosperm Welwitschia mirabilis in the Namib Desert, and whether this island effect varied with climate and with gender of plants....
Article
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Understanding the spatial and temporal patterns of human pressures provides a foundation for understanding interactions between human and environment and managing human activities for a sustainable development. This study is the first attempt focused within China at calculating the spatial–temporal human footprint and its driving forces in a highly...
Article
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Microbial biogeographical patterns in Mediterranean ecosystems are becoming widely documented; however, the influences of slope aspect on the microbial community composition and structure are poorly understood. This study tested the hypotheses that slope aspect and organic matter content would influence microbial diversity patterns and distribution...
Preprint
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The paradoxical pattern of a cytokine storm seem mostly in older COVID19 patients might be explicable through potentiation by an earlier and now-extinct virus, by analogy with the potentiation seen in other infections such as dengue.
Article
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The soil fungal ecology of the southern Gobi region of Mongolia has been little studied. We utilized the ITS1 region from soil DNA to study possible influences soil metal concentrations on soil fungal community variation. In the sample network, a distinctive fungal community was closely associated with high zinc (Zn), lead (Pb), and copper (Cu) con...
Article
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Depth patterns of soil microbial distribution have not been well characterized and little is known about the balance between stochastic and deterministic processes in shaping microbial community through soil profiles. We examined how the composition, diversity, and assembly processes of bacterial communities change to a depth of 4 m along three cor...
Article
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A resumption of climate warming in maritime Antarctica, arising from continued greenhouse gas emissions to the atmosphere, is predicted to lead to further expansions of plant populations across the region, with consequent increases in nutrient inputs to soils. Here, we test the main and interactive effects of warming, applied with open top chambers...
Article
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Deinococcus is a genus of soil bacteria known for radiation resistance. However, the effects of radiation exposure on its community structure are unknown. We exposed soil to three levels of gamma radiation, 0.1 kGy/h (low), 1 kGy/h (medium), and 3 kGy/h (high), once a week for 6 weeks and then extracted soil DNA for 16S rRNA amplicon sequencing. We...
Article
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It has been widely accepted that there is a distance‐decay pattern in the soil microbiome. However, few studies have attempted to interpret the microbial distance‐decay pattern from the perspective of quantifying underlying processes. In this study, we examined the processes governing bacterial community assembly at multiple spatial scales in maize...
Article
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Despite the extensive, ongoing conversion of tropical forests to rubber plantation, the effects of this land use change on soil fungal community diversity and composition are still poorly known. We compared a network of sites of tropical forest in southern Yunnan, China, with a network of rubber plantation sites originally derived from this forest....
Article
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Soil fungi have many important ecological functions, however, their life strategies and interactions in manure fertilized soils are not well understood. The aim of this study was to investigate the effects of biochar amendment on the fungal life strategies and species interactions in ryegrass (Lolium perenne L.) rhizosphere soil by high-throughput...
Article
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The vast diversity of soil bacteria provides essential ecosystem services that support agricultural production. Variation in the diversity and composition of soil biota may have predictive values for soil nutrient cycling and resilience of ecosystem services, thus providing valuable insights to improve food production. The North China Plain (NCP) i...
Article
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Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of 60Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAS...
Article
Full-text available
The South African Fynbos is the smallest floristic kingdom with high levels of endemism and where fire dominates the landscape. However, drivers of soil microbial distribution and diversity are still poorly understood. This study aims to highlight the biogeographical patterns of bacterial and fungal communities and elucidate the mechanisms that med...
Article
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Little is known of how fungal distribution ranges vary with elevation. We studied fungal diversity and community composition from 740 to 2940 m above sea level on Mt. Norikura, Japan, sequencing the ITS2 region. There was a clear trend, repeated across each of the fungal phyla (Basidiomycota, Ascomycota, Zygomycota, Chytridomycota and Glomeromycota...
Article
Full-text available
Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of 60Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAS...