Host-associated bacterial communities can function as an important line of defence against pathogens in animals and plants. Empirical evidence and theoretical predictions suggest that species-rich communities are more resistant to pathogen invasions. Yet, the underlying mechanisms are unclear. Here, we experimentally test how the underlying resource competition networks of resident bacterial communities affect invasion resistance to the plant pathogen Ralstonia solanacearum in microcosms and in tomato plant rhizosphere. We find that bipartite resource competition networks are better predictors of invasion resistance compared with resident community diversity. Specifically, communities with a combination of stabilizing configurations (low nestedness and high connectance), and a clear niche overlap with the pathogen, reduce pathogen invasion success, constrain pathogen growth within invaded communities and have lower levels of diseased plants in greenhouse experiments. Bacterial resource competition network characteristics can thus be important in explaining positive diversity–invasion resistance relationships in bacterial rhizosphere communities.

The impact of agricultural management on global warming potential (GWP) and greenhouse gas intensity (GHGI) is not well documented. A long-term fertilizer experiment in Chinese double rice-cropping systems initiated in 1990 was used in this study to gain an insight into a complete greenhouse gas accounting of GWP and GHGI. The six fertilizer treatments included inorganic fertilizer [nitrogen and phosphorus fertilizer (NP), nitrogen and potassium fertilizer (NK), and balanced inorganic fertilizer (NPK)], combined inorganic/organic fertilizers at full and reduced rate (FOM and ROM), and no fertilizer application as a control. Methane (CH 4 ) and nitrous oxide (N 2 O) fluxes were measured using static chamber method from November 2006 through October 2009, and the net ecosystem carbon balance was estimated by the changes in topsoil (0-20 cm) organic carbon (SOC) density over the 10-year period 1999-2009. Longterm fertilizer application significantly increased grain yields, except for no difference between the NK and control plots. Annual topsoil SOC sequestration rate was estimated to be 0.96 t C ha À1 yr À1 for the control and 1.01-1.43 t C ha À1 yr À1 for the fertilizer plots. Long-term inorganic fertilizer application tended to increase CH 4 emissions during the flooded rice season and significantly increased N 2 O emissions from drained soils during the nonrice season. Annual mean CH 4 emissions ranged from 621 kg CH 4 ha À1 for the control to 1175 kg CH 4 ha À1 for the FOM plots, 63-83% of which derived from the late-rice season. Annual N 2 O emission averaged 1.15-4.11 kg N 2 O-N ha À1 in the double rice-cropping systems. Compared with the control, inorganic fertilizer application slightly increased the net annual GWPs, while they were remarkably increased by combined inorganic/organic fertilizer application. The GHGI was lowest for the NP and NPK plots and highest for the FOM and ROM plots. The results of this study suggest that agricultural economic viability and GHGs mitigation can be simultaneously achieved by balanced fertilizer application.

Plant-pathogen interactions are shaped by multiple environmental factors, making it difficult to predict disease dynamics even in relatively simple agricultural monocultures. Here, we explored how variation in the initial soil microbiome predicts future disease outcomes at the level of individual plants. We found that the composition and functioning of the initial soil microbiome predetermined whether the plants survived or succumbed to disease. Surviving plant microbiomes were associated with specific rare taxa, highly pathogen-suppressing Pseudomonas and Bacillus bacteria, and high abundance of genes encoding antimicrobial compounds. Microbiome-mediated plant protection could subsequently be transferred to the next plant generation via soil transplantation. Together, our results suggest that small initial variation in soil microbiome composition and functioning can determine the outcomes of plant-pathogen interactions under natural field conditions.

Plant pathogenic bacteria cause high crop and economic losses to human societies [1][2][3] . Infections by such pathogens are challenging to control as they often arise through complex interactions between plants, pathogens and the plant microbiome 4,5 . This natural ecosystem is rarely studied experimentally at the microbiome-wide scale, and consequently we poorly understand how taxonomic and functional microbiome composition and the resulting ecological interactions affect pathogen growth and disease outbreak. Here we combine DNA-based soil microbiome analysis with in vitro and in planta bioassays to show that competition for iron via secreted siderophore molecules is a good predictor of microbe-pathogen interactions and plant protection. We examined the ability of 2150 individual bacterial members of 80 rhizosphere microbiomes, covering all major phylogenetic lineages, to suppress the bacterium Ralstonia solanacearum, a global phytopathogen capable of infecting various crops 6,7 . We found that secreted siderophores altered microbiome-pathogen interactions from complete pathogen suppression to strong facilitation. Rhizosphere microbiome members with growth-inhibitory siderophores could often suppress the pathogen in vitro, in natural and greenhouse soils, and protect tomato plants from infection.Conversely, rhizosphere microbiome members with growth-promotive siderophores were often inferior in competition and facilitated plant infection by the pathogen. Because siderophores are a #

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