The Effect of Plasma Activated Water on the Rhizosphere Composition of Arabidopsis and Solanum lycopersicum

The Effect of Plasma Activated Water on the Rhizosphere Composition of Arabidopsis and Solanum lycopersicum | bioRxiv /* */ /* */ <!-- <!-- /*! * yepnope1.5.4 * (c) WTFPL, GPLv2 */ (function(a,b,c){function d(a){return"[object Function]"==o.call(a)}function e(a){return"string"==typeof a}function f(){}function g(a){return!a||"loaded"==a||"complete"==a||"uninitialized"==a}function h(){var a=p.shift();q=1,a?a.t?m(function(){("c"==a.t?B.injectCss:B.injectJs)(a.s,0,a.a,a.x,a.e,1)},0):(a(),h()):q=0}function i(a,c,d,e,f,i,j){function k(b){if(!o&&g(l.readyState)&&(u.r=o=1,!q&&h(),l.onload=l.onreadystatechange=null,b)){"img"!=a&&m(function(){t.removeChild(l)},50);for(var d in y[c])y[c].hasOwnProperty(d)&&y[c][d].onload()}}var j=j||B.errorTimeout,l=b.createElement(a),o=0,r=0,u={t:d,s:c,e:f,a:i,x:j};1===y[c]&&(r=1,y[c]=[]),"object"==a?l.data=c:(l.src=c,l.type=a),l.width=l.height="0",l.onerror=l.onload=l.onreadystatechange=function(){k.call(this,r)},p.splice(e,0,u),"img"!=a&&(r||2===y[c]?(t.insertBefore(l,s?null:n),m(k,j)):y[c].push(l))}function j(a,b,c,d,f){return q=0,b=b||"j",e(a)?i("c"==b?v:u,a,b,this.i++,c,d,f):(p.splice(this.i++,0,a),1==p.length&&h()),this}function k(){var a=B;return a.loader={load:j,i:0},a}var l=b.documentElement,m=a.setTimeout,n=b.getElementsByTagName("script")[0],o={}.toString,p=[],q=0,r="MozAppearance"in l.style,s=r&&!!b.createRange().compareNode,t=s?l:n.parentNode,l=a.opera&&"[object Opera]"==o.call(a.opera),l=!!b.attachEvent&&!l,u=r?"object":l?"script":"img",v=l?"script":u,w=Array.isArray||function(a){return"[object Array]"==o.call(a)},x=[],y={},z={timeout:function(a,b){return b.length&&(a.timeout=b[0]),a}},A,B;B=function(a){function b(a){var a=a.split("!"),b=x.length,c=a.pop(),d=a.length,c={url:c,origUrl:c,prefixes:a},e,f,g;for(f=0;f<d;f++)g=a[f].split("="),(e=z[g.shift()])&&(c=e(c,g));for(f=0;f<b;f++)c=x[f](c);return c}function g(a,e,f,g,h){var i=b(a),j=i.autoCallback;i.url.split(".").pop().split("?").shift(),i.bypass||(e&&(e=d(e)?e:e[a]||e[g]||e[a.split("/").pop().split("?")[0]]),i.instead?i.instead(a,e,f,g,h):(y[i.url]?i.noexec=!0:y[i.url]=1,f.load(i.url,i.forceCSS||!i.forceJS&&"css"==i.url.split(".").pop().split("?").shift()?"c":c,i.noexec,i.attrs,i.timeout),(d(e)||d(j))&&f.load(function(){k(),e&&e(i.origUrl,h,g),j&&j(i.origUrl,h,g),y[i.url]=2})))}function h(a,b){function c(a,c){if(a){if(e(a))c||(j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}),g(a,j,b,0,h);else if(Object(a)===a)for(n in m=function(){var b=0,c;for(c in a)a.hasOwnProperty(c)&&b++;return b}(),a)a.hasOwnProperty(n)&&(!c&&!--m&&(d(j)?j=function(){var a=[].slice.call(arguments);k.apply(this,a),l()}:j[n]=function(a){return function(){var b=[].slice.call(arguments);a&&a.apply(this,b),l()}}(k[n])),g(a[n],j,b,n,h))}else!c&&l()}var h=!!a.test,i=a.load||a.both,j=a.callback||f,k=j,l=a.complete||f,m,n;c(h?a.yep:a.nope,!!i),i&&c(i)}var i,j,l=this.yepnope.loader;if(e(a))g(a,0,l,0);else if(w(a))for(i=0;i (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0];var j=d.createElement(s);var dl=l!='dataLayer'?'&l='+l:'';j.src='//www.googletagmanager.com/gtm.js?id='+i+dl;j.type='text/javascript';j.async=true;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-M677548'); Skip to main content Home About Submit ALERTS / RSS Search for this keyword Advanced Search New Results The Effect of Plasma Activated Water on the Rhizosphere Composition of Arabidopsis and Solanum lycopersicum Jon Kizer , Xavious Allen , Conner Robinson , View ORCID Profile Amy Grunden , View ORCID Profile Katharina Stapelmann , View ORCID Profile Marcela Rojas-Pierce doi: https://doi.org/10.1101/2025.10.15.682576 Jon Kizer 1 Department of Plant and Microbial Biology, North Carolina State University , Raleigh, North Carolina, United States of America Find this author on Google Scholar Find this author on PubMed Search for this author on this site Xavious Allen 1 Department of Plant and Microbial Biology, North Carolina State University , Raleigh, North Carolina, United States of America Find this author on Google Scholar Find this author on PubMed Search for this author on this site Conner Robinson 2 Department of Nuclear Engineering, North Carolina State University , Raleigh, North Carolina, United States of America Find this author on Google Scholar Find this author on PubMed Search for this author on this site Amy Grunden 1 Department of Plant and Microbial Biology, North Carolina State University , Raleigh, North Carolina, United States of America Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Amy Grunden For correspondence: mrojasp{at}ncsu.edu kstapel{at}ncsu.edu amgrunde{at}ncsu.edu Katharina Stapelmann 2 Department of Nuclear Engineering, North Carolina State University , Raleigh, North Carolina, United States of America Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Katharina Stapelmann For correspondence: mrojasp{at}ncsu.edu kstapel{at}ncsu.edu amgrunde{at}ncsu.edu Marcela Rojas-Pierce 1 Department of Plant and Microbial Biology, North Carolina State University , Raleigh, North Carolina, United States of America Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Marcela Rojas-Pierce For correspondence: mrojasp{at}ncsu.edu kstapel{at}ncsu.edu amgrunde{at}ncsu.edu Abstract Full Text Info/History Metrics Supplementary material Preview PDF ABSTRACT The emerging field of plasma agriculture investigates the potential benefit of non-thermal plasma (NTP) for agricultural practices. NTP-treated water, referred to as plasma activated water (PAW), has been proposed as a sustainable alternative to conventional nitrogen (N) fertilizers. Growing demand for N fertilizer is concomitant with increased global food demands. PAW contains nitrate (NO 3 - ) and reactive oxygen species, such as hydrogen peroxide (H 2 O 2 ), which are fixed from atmospheric molecules via NTP. While early studies report positive effects of PAW on plant growth, its influence on plant-associated microbial communities remains poorly understood. Here, we compared the impacts of PAW or NO 3 - solutions on the rhizosphere microbial community of Arabidopsis thaliana and Solanum lycopersicum . PAW was generated by a radio frequency (RF) glow discharge plasma source and contained no measurable ROS, while the control solution contained an equivalent concentration of NO 3 - . No significant differences in alpha diversity were detected in either plant species microbiome after 5 weeks of treatment when grown in non-commercial potting substrate. Significant dissimilarity was found in terms of beta diversity, but the relative abundance of the sequenced genera suggested no functional differences in rhizosphere communities. Overall, PAW treatment did not adversely impact the rhizosphere microbiome in either Arabidopsis or tomato. These results support the use of PAW as an alternative N-fertilizer, though outcomes may differ for PAW solutions containing ROS. INTRODUCTION Global food demand continues to rise, driving increased use of Nitrogen (N) fertilizers ( Lassaletta et al., 2014 ). Synthetic fertilizers represent the largest portion of N-fertilizers utilized globally in agriculture ( Lassaletta et al., 2014 ; Menegat et al., 2022 ). The energy-intensive Haber-Bosch process, used to fix atmospheric N, contributes 2.9 tons of atmospheric CO 2 globally ( Menegat et al., 2022 ; M. Wang et al., 2021 ), and is the primary method for industrial synthetic N fertilizer production. This reliance on unsustainable fertilizer production has spurred development of greener alternatives to generate N fertilizers while also meeting global demands ( Chen et al., 2018 ). Plasma agriculture applies non-thermal plasmas (NTP) to fix atmospheric N 2 into NO 3 - , a plant-available form. This provides a potential low-carbon alternative for fertilizer production. Treating water with NPT produces Plasma-Activated Water (PAW) or Plasma-Treated Water (PTW), a liquid fertilizer containing nitrate (NO 3 - ). Depending on the production method, the resulting PAW solution may contain concentrations of reactive oxygen species (ROS) such as hydrogen peroxide (H 2 O 2 ) and superoxide (O 2 - ) or reactive nitrogen species (RNS) such as nitric oxide (NO) or peroxynitrite (ONOO - ). A healthy plant-associated rhizosphere microbiome is vital for robust plant growth as it is important for nutrient cycling and availability for plant use ( Berendsen et al., 2012 ; Berg et al., 2014 ; Hein et al., 2008 ; Jafariyan & Zarea, 2016 ; Ney et al., 2019 ; Richardson & Simpson, 2011 ; Schneijderberg et al., 2020 ; Zhang et al., 2022 ). At the same time, the plant and soil environment strongly influence the diversity and function of the rhizosphere microbiome ( Ai et al., 2015 ; Berendsen et al., 2012 ; Berg et al., 2014 ). Given that fertilizer application has major impacts on the plant and soil environment, it also affects the rhizosphere microbiome composition and performance in crop plants ( Igiehon & Babalola, 2018 ; Shi et al., 2020 ; Zhu et al., 2016 ). For example, Zhu et al. reported a significant correlation between N application rate and microbial abundance in the rhizosphere. Increased N fertilizer application rates are also correlated with increased rates of exudates released from the plant host roots ( Zhu et al., 2016 ). Additionally, since ROS play a key role in how plants respond to different environmental cues ( Tsukagoshi et al., 2010 ), introduction of ROS and RNS from PAW (together referred to as RONS) can alter stress signaling pathways and growth or the interactions with the microbiome ( Berrios & Rentsch, 2022 ; Jafariyan & Zarea, 2016 ). It is therefore important to evaluate the impact of PAW on plant-associated microbiomes. To that end, in this study, we investigate the effect of PAW without measurable ROS on rhizosphere microbiomes of Arabidopsis and tomato. RESULTS Rhizosphere Microbiome Analysis of Arabidopsis thaliana Understanding whether PAW treatment alters the plant-associated microbiome is important to ascertain its potential as a N fertilizer substitute. We first tested whether PAW treatment had any effect on the Arabidopsis rhizosphere microbiome. A Radio Frequency (RF) glow discharge plasma source ( Byrns et al., 2012 ; Lindsay et al., 2014 ) was used to generate PAW with 4.8 mM (310 ppm) of NO 3 - , which is sufficient for Arabidopsis growth ( Boer et al., 2020 ). This PAW was specifically produced with no detectable H 2 O 2 levels, given the negative effect of ROS-containing PAW on Arabidopsis root growth ( Kizer et al., 2025 ). Wild-type Arabidopsis seedlings were first germinated in sterile gel media before transplanting into substrate. The substrate was a mixture of commercial peatmoss with vermiculite and perlite not previously exposed to Arabidopsis plants, and therefore, the recruited microbes originate from the substrate itself or the seedlings ( Truyens et al., 2013 ; Truyens et al., 2015 ). Plants were treated weekly with either PAW or NO 3 - control solution as the only source of N. Plant roots were harvested after 5 weeks for rhizosphere microbiome analysis. DNA was extracted from rhizosphere samples and underwent 16S rRNA amplicon sequencing. The highly-variable V4 region was amplified using 515f (Parada) and 806r (Apprill) primers ( Apprill et al., 2015 ; Parada et al., 2016 ), as this allows for effective classification accuracy and adequate diversity coverage with limited bias ( Claesson et al., 2010 ; Walters et al., 2015 ). Amplicon sequencing of the V4 region with these primers has become a standard for sequencing of plant-associated bacteria ( Gilbert et al., 2014 ; Walters et al., 2015 ), and provides adequate coverage ( Breidenbach et al., 2016 ). Taxonomic identification was performed at the genus level to provide meaningful insight into the microbiome community structure under the conditions tested. Both Shannon and Simpson indices were used to determine the microbial biodiversity. Alpha diversity analysis showed that both PAW-treated and NO 3 - -treated plants exhibited similar species richness in the rhizosphere microbial population. A Kruskal-Wallis test yielded statistically insignificant p-values at a 0.05 alpha of 0.4497 and 0.2899 for Shannon and Simpson statistics, respectively ( Fig. 1 ). This indicated that PAW treatment did not affect overall species richness in Arabidopsis-associated rhizosphere microbial community when compared to the NO 3 - control. Download figure Open in new tab Figure 1. Rhizosphere microbiomes from Arabidopsis treated with PAW or the nitrate control exhibit similar taxa richness. Arabidopsis rhizosphere microbiomes were identified from plants treated with PAW containing 4.8 mM NO 3 - or a control with equivalent NO 3 - concentration for 5 weeks. Amplicon Sequence Variants (ASV) were derived from sequencing data and Shannon and Simpson statistics were calculated and plotted from the ASVs. A student’s T-test was performed to evaluate statistical significance. N= 10 samples per treatment. Beta diversity of the PAW- and nitrate-treated plants was calculated using the Bray-Curtis dissimilarity method. The resulting distance statistic matrix was suitable for exploratory investigations such as the one conducted for this study ( Hein et al., 2008 ; Schneijderberg et al., 2020 ). From the distance matrix, the data was plotted using Non-metric Multi-Dimensional Scaling (NMDS) and Principal Coordinate Analysis (PCoA) to scale and for visualization. The NMDS plot yielded a partial crossover indicating that there are shared microbial community members across between the two treatments ( Fig. 2 A ). However, further analysis and visualization with the PCoA plot showed separation of the two treatments with 9.4% and 8.2% for Axis 1 and 2, respectively ( Fig. 2B ). An R-package Residual Randomization in a Permutation Procedure (RRPP) analysis was then performed as a post-hoc test utilizing the distance matrix, which determined a statistically significant result at a 0.05 alpha, which indicates that there is significant dissimilarity in the rhizosphere bacteria composition between treatments. However, this variation may not be reflected in functional differences in rhizosphere microbiome performance because of functional redundancy that exists within the two Arabidopsis rhizosphere community structures. Download figure Open in new tab Figure 2. Rhizosphere microbiomes from Arabidopsis treated with PAW or the nitrate control exhibit dissimilarity in community makeup. Arabidopsis rhizosphere microbiomes were identified from plants treated with PAW (4.8 mM NO 3 - ) or a solution of equivalent NO 3 - concentration for 5 weeks. Amplicon Sequence Variants (ASV) were derived from the sequencing data. Bray-Curtis distances were calculated and plotted via Non-metric Multi-Dimensional Scaling (NMDS) (top) and a Principal Coordinate Analysis (PCoA) (bottom). A residual randomization in permutation procedures (RRPP) analysis was conducted in R to find statistical significance. N= 10 samples per treatment Lastly, taxonomic data from the Silva bacterial 16S rRNA database was utilized to determine the identity and relative abundance of each Amplicon Sequence Variants (ASVs) in our samples at the genus taxonomic level ( Quast et al., 2012 ). The Phyloseq R package ( McMurdie & Holmes, 2013 ) was used for analysis, and each identified taxa was grouped by family. The top 50 taxa were then plotted and represented for each sample ( Fig. 3 ). Interestingly, bacteria of the combined genus Burkholderia-Caballeronia-Paraburkholderia (BCP) were prominently represented across both treatment types ( Fig. 3 ). This family has been associated with plant growth-promoting function ( O’Sullivan & Mahenthiralingam, 2005 ; Suárez-Moreno et al., 2012 ; K. Wang et al., 2021 ). Download figure Open in new tab Figure 3. The rhizosphere microbiome from Arabidopsis treated with PAW or the control treatment exhibit similar bacterial families represented in the 50 most abundant taxa. Arabidopsis rhizosphere microbiomes were identified from plants treated with PAW (4.8 mM NO 3 - ) or a solution of equivalent NO 3 - concentration for 5 weeks and Amplicon Sequence Variants (ASV) were derived from the sequencing data. Taxonomic identities were assigned to ASVs with the Phyloseq R package. The 50 ASVs with the greatest relative abundance from each sample were plotted and grouped by genus. Rhizosphere Microbiome Analysis of Solanum lycopersicum The effect of PAW treatment on the rhizosphere microbiome of a crop species, S. lycopersicum , was also investigated. PAW containing 6.5 mM (400 ppm) NO 3 - and no detectable H 2 O 2 was used given the higher N need of this crop species. The same substrate mixture was used to control nutrients for this experiment, and seeds were directly planted into substrate. A 0.75x concentrated Hoagland solution without N was added biweekly to provide all necessary nutrients except N. Tomato seedlings were treated weekly with PAW or the NO 3 - control solution, and all plants were harvested after 5 weeks. Plant height, total dry biomass, and root:shoot dry biomass ratio were measured, and no differences were detected between PAW-treated tomatoes and the NO 3 - control (Supplemental Fig. 1). Ten tomato seedlings per treatment were removed, and the substrate attached to the roots was harvested. Microbial genetic material from the rhizosphere compartment of the plant-associated microbiome was analyzed in the same manner as was performed for the Arabidopsis microbiome analysis. When comparing the rhizosphere microbiome of PAW-treated samples to that of the NO 3 - control, the Shannon diversity analysis indicated significant differences (p = 0.0413), while the Simpson diversity analysis did not (p = 0.3643). Significance was calculated at a 0.05 alpha using a student’s T-test ( Fig. 4 ). These small differences suggested limited differences in species richness between the two treatments. The Shannon index correlates to species richness and evenness, but all genera are weighed equally, causing rarer genera, which are common in microbial studies, to potentially bias the statistic ( Hill et al., 2003 ; Hong et al., 2006 ; Shannon, 1948 ). With the Shannon index showing significance, but the Simpson showing the contrary, this implies there may be a number of taxa found only in a small number of our samples that bias the Shannon index. Download figure Open in new tab Figure 4. The rhizosphere microbiomes of tomato treated with PAW or the control treatment exhibit mild variation in taxa richness. Tomato plant rhizosphere microbiomes were identified from plants treated with PAW (6.5 mM NO 3 - ) or a solution of equivalent NO 3 - concentration for 5 weeks and Amplicon Sequence Variants (ASV) were derived from the sequencing data and Shannon and Simpson statistics were calculated and plotted from the ASVs. A student’s T-test was performed to evaluate statistical significance. N= 10 samples per treatment Next, beta diversity was determined by Bray-Curtis dissimilarities between treatment groups, and the distance matrix was plotted utilizing NMDS and PCoA. The NMDS plot exhibited visual separation between the two treatments ( Fig. 5A ), suggesting dissimilarity in bacterial genera present between plants treated with PAW versus the NO 3 - control. The PCoA plot provided visual confirmation with calculated separation with Axis1 and 2 values of 39% and 17.9%, respectively ( Fig. 5B ). While both treatments clustered separately, the two clusters were in close proximity. An RRPP analysis of the distance matrix was performed to confirm statistical significance. Similar to Arabidopsis, this analysis identified differences in bacterial genera that are present in the rhizosphere of PAW-treated tomato compared to the control. Download figure Open in new tab Figure 5. The rhizosphere microbiomes of tomato treated with PAW or the control treatment exhibit dissimilarity in community makeup. Tomato plant rhizosphere microbiomes were identified from plants treated with PAW (6.5 mM NO 3 - ) or a solution of equivalent NO 3 - concentration for 5 weeks. Amplicon Sequence Variants (ASV) were derived from the sequencing data. Bray-Curtis distances were calculated and plotted via Non-metric Multi-Dimensional Scaling (NMDS) (top) and a Principal Coordinate Analysis (PCoA) (bottom). A residual randomization in permutation procedures (RRPP) analysis was conducted in R to find statistical significance. N= 10 samples per treatment Taxonomic data was provided from the ASVs processed through the DADA2 pipeline. The Phyloseq R package ( McMurdie & Holmes, 2013 ) was utilized to determine relative abundance of each taxa across treatments. The top 20 taxa were plotted and presented for each sample ( Fig. 6 ). Both PAW and NO 3 - treatments resulted in a similar representation of different bacterial genera. Notably, tomato seedlings treated with PAW had the Puia genus represented in the top 20 ASVs while this was observed in only a single seedling treated with the NO 3 - control. While most genera represented amongst the most dominant bacteria are conserved across both treatment groups, the addition of Puia coupled with the significant differences in beta diversity calculations suggest that tomato seedlings treated with PAW possess identifiable differences in terms of rhizosphere microbial makeup. Download figure Open in new tab Figure 6. The rhizosphere microbiomes of tomato treated with PAW or the control treatment exhibit similar bacterial genera represented in the 20 most abundant taxa. Tomato plant rhizosphere microbiomes were identified from plants treated with PAW (6.5 mM NO 3 - ) or a solution of equivalent NO 3 - concentration for 5 weeks and Amplicon Sequence Variants (ASV) were derived from the sequencing data. Taxonomic identities were assigned to ASVs with the Phyloseq R package. The 20 ASVs with the greatest relative abundance from each sample were plotted and grouped by genus. DISCUSSION The root microbiome can be crucial to plant health due to its ability to facilitate nutrient availability and respond to changes in soil conditions ( Berendsen et al., 2012 ; Berg et al., 2014 ; Hein et al., 2008 ; Jafariyan & Zarea, 2016 ; Ney et al., 2019 ; Richardson & Simpson, 2011 ; Schneijderberg et al., 2020 ). The diversity and health of the plant-associated microbiome are contingent on environmental factors ( Ai et al., 2015 ; Berendsen et al., 2012 ; Berg et al., 2014 ). Additionally, variations in root exudates promote the association of certain microbes versus others ( Badri et al., 2013 ; Broeckling et al., 2008 ; Chaparro et al., 2013 ; Chaparro et al., 2012 ; Gregory, 2007 ; Micallef et al., 2009 ; Sasse et al., 2018 ; Zhao et al., 2021 ). In a crop system, the addition of fertilizers impact the state of the plant-associated microbiome ( Igiehon & Babalola, 2018 ; Shi et al., 2020 ; Zhu et al., 2016 ) with N fertilizer application rates positively correlated with root exudation rates ( Zhu et al., 2016 ). The effect of fertilizers on microbiome health is relevant when evaluating the efficacy of PAW as an N fertilizer. PAW is a potential alternative to other less sustainable N-fertilizers. Several studies have shown that PAW has potential enhancements to plant growth when compared to a nitrate-depleted control ( Cortese et al., 2021 ; Cui et al., 2022 ; Cui et al., 2019 ; Kučerová et al., 2021 ; Kučerová et al., 2019 ; Ndiffo Yemeli et al., 2021; Panngom et al., 2018 ; Škarpa et al., 2020 ). From this study, tomato plants supplemented weekly with PAW exhibited comparable growth to those grown with the equivalent NO 3 - control, which indicates that PAW-treatment can substitute a synthetic fertilizer regime. Studies have already captured the potential effects of PAW on plant growth, however PAW’s impacts on the plant-associated microbiome are relatively unexplored. Direct NTP treatment on Arabidopsis seedlings resulted in changes in microbial community make-up with Mycobacteriaceae being greatly reduced and Bacillaceae abundance being enhanced ( Tamošiūnė et al., 2020 ). Bacteria genera such as Pseudomonas and Paenibacillus exhibited increased abundance in mature Arabidopsis that grew from NTP-treated seeds ( Tamošiūnė et al., 2020 ), which are known to be beneficial and promote growth ( Grady et al., 2016 ; Santoyo et al., 2012 ). Changes in microbial community make-up were also observed in seeds directly treated with NTP ( Ji et al., 2019 ). In this study, long-term treatment with PAW and the NO 3 - control did not indicate changes in the functional community makeup of the rhizosphere. Interestingly, bacteria associated with NO 3 - transformations such as those of the Xanthobacteraceae family were represented in the most abundant taxa for both Arabidopsis and tomato which is expected in an N-rich soil environment ( Ward, 2013 ; Yuan et al., 2015 ). Establishing potential impacts of PAW treatment on rhizosphere composition and function was the focus of this study in light of extensive research on the rhizosphere microbiome and its important role in maintaining plant health ( Hein et al., 2008 ; Jafariyan & Zarea, 2016 ; Schneijderberg et al., 2020 ). In this study, both Arabidopsis and tomato showed similarities in terms of species richness and community make-up between PAW and control-treated plants. This is in contrast to studies in Brassicaceae where changes in N fertilizer source resulted in altered rhizosphere communities by affecting microbe recruitment ( Li et al., 2023 ; O’Brien et al., 2018 ; Windisch et al., 2021 ). Additionally, changes in N fertilizers also affected the facilitation of nutrient uptake, including phosphorus via plant-associated microbes in maize ( Mang et al., 2023 ). Even in S. lycopersicum , treatments with different synthetic N fertilizers with different chemical composition resulted in an overall enrichment in rhizosphere biodiversity including beneficial Actinobacteria ( Caradonia et al., 2019 ). The limited changes in the rhizosphere composition observed in the PAW-treated plants supports use of PAW as an alternative fertilizer, at least for PAWs with minimal ROS. Depending on varying factors in the plasma-treatment method, ROS are commonly produced in PAW ( Cui et al., 2022 ; Iseni et al., 2016 ; Kučerová et al., 2019 ; Ran, Zhou, Wang, et al., 2024). ROS in PAW, such as H 2 O 2 ( Ghimire et al., 2018 ) or OH radicals ( Lamichhane et al., 2019 ), have shown antimicrobial effects ( Graves, 2012 ; Zhang et al., 2018 ) leading to PAW being utilized in industrial sterilization ( Zhang et al., 2012 ; Ziuzina et al., 2013 ) and plasma medicine ( Hayashi et al., 2006 ). Plasma capillary discharge yielding high ROS levels can reduce up to 99.6% E. coli load in water ( Hong et al., 2010 ). PAW also has antimicrobial activity against plant pathogens ( Ghimire et al., 2024 ; Ran, Zhou, Dong, et al., 2024). However, PAW without measurable ROS was utilized in this study since ROS in PAW can adversely affect plant growth ( Cui et al., 2022 ; Cui et al., 2019 ; Ka et al., 2021 ; Kizer et al., 2025 ; Zhou et al., 2018 ). Therefore, other PAW solutions containing ROS may result in changes in the microbiome not captured in this study. Future work should carefully consider the ROS content of PAW when studying plant-associated microbial communities. This study found that under both treatments, Burkholderiaceae bacteria were amongst the most abundant taxa for both Arabidopsis and tomato, specifically those belonging to the combined BCP genus. The BCP group consists of gram-negative bacteria that can either be free-living or endophytic. Bacteria of the Caballeronia and Paraburkhoderia genera exhibit nitrogen-fixing functions in association with various plant species ( Paulitsch et al., 2019 ; Puri et al., 2020 ; Suárez-Moreno et al., 2012 ). In particular, BCP bacteria promote plant growth when associated with Arabidopsis ( Adhikari et al., 2019 ; Huang et al., 2017 ; Ruiz et al., 2025 ; K. Wang et al., 2021 ). NO 3 - replete conditions typically result in higher abundance of this family ( Konishi et al., 2017 ). The Burkholderiaceae family is ubiquitous and functionally diverse, with some members isolated as plant pathogens ( Adhikari et al., 2019 ; Jeong et al., 2003 ; Mannaa et al., 2019 ), while others act as plant growth promoters ( Konishi et al., 2017 ; O’Sullivan & Mahenthiralingam, 2005 ; Suárez-Moreno et al., 2012 ). Given that samples were sequenced at the genera level, an accurate account of the specific species present and their functions is not available in this study. Further studies are needed to determine whether PAW treatment can result in recruitment of specific Burkholderiaceae species. Tomato seedlings treated with PAW exhibited limited differences in rhizosphere microbial composition compared to nitrate treated samples. Specifically, the Puia genus was amongst the most abundant ASVs for PAW-treated samples. Puia is a relatively unstudied genus of the larger Chitinophagaceae family, which was represented by two other genera in both treatments (Supplemental Fig. 3A). Only Puia dinghuensis isolated from a forest soil has been characterized ( Lv et al., 2017 ). Other members of the Chitinophagaceae have been shown to have beneficial properties for plant growth. For example, these bacteria often produce of plant growth-promoting compounds such as indole-3-acetic acid ( Wang et al., 2025 ), they can break down chitin to release plant-available forms of nutrients ( Anzuay et al., 2021 ; Hui et al., 2020 ; Jia et al., 2024 ), and can help control pathogens ( Lopez-Nuñez et al., 2025 ; Nishisaka et al., 2025 ). It is unclear whether the small changes in Puia recruitment would be beneficial to PAW-treated plants. Overall, this study determined that plants treated with PAW have similar rhizosphere species richness compared to those treated with an inorganic N fertilizer. While limited differences were detected in the respective microbial communities, we found strong similarities when comparing the most abundant taxa. This study constitutes early research on the effects of PAW on the plant-associated microbiome and provides findings that lend support for the use of PAW as a N fertilizer since disruption of plant rhizosphere was not observed for either Arabidopsis or tomato. Further investigation with agricultural soil samples and varying compositions of PAW may provide greater insight as to practical effects of PAW on the plant-associated microbiome. MATERIALS AND METHODS PAW production PAW was produced as previously reported ( Kizer et al., 2025 ). using an atmospheric radio frequency (RF) glow discharge plasma. In brief, bulk diH 2 O volumes were exposed to the plasma that was generated by an AE OVAtion 35162 RF at 250 W. Air was flowed down the coaxial electrode, toward the water surface at a rate of ≤ 1 slm. To optimize NO 3 - content, a large external volume of water (≥ 2 L) was circulated through the plasma chamber, which was kept open to improve ventilation, and the distance between the water surface and electrode was set to minimize reflected power (20–40 W reflected at 1.5 cm). Under these conditions, the plasma was consistently able to produce aqueous NO 3 - at a rate of 2 mg/min, and treatment times were adjusted accordingly to achieve the desired concentration for the target volume. The chemical composition was measured colorimetrically and then combined with untreated diH 2 O to obtain the final desired PAW volumes and chemistries. The final PAW would also be tested colorimetrically, to confirm their composition. For each step NO 3 - , NO 2 - , H 2 O 2 , and NH 4 + were tested for in triplicate using the commercially available Supelco test kits: 1.09713, 1.14776, 1.18789 and 1.14752, respectively. Absorbance values were obtained using an UV-VIS-NIR light source (Ocean Optics DH-2000-BAL) in conjunction with a spectrometer (Ocean Optics QE65 Pro) and a cuvette holder (Ocean Optics CUV-UV). These absorbances were converted to concentrations using stock solution based standard curves prepared in advance. PAW was neutralized with 1M KOH solution to increase the pH to 5.7, a plant-viable pH. Neutralization maintained stability of the solution for storage. PAW was stored in the dark at room temperature for up to 2 weeks, which is unlikely to result in significant changes in nitrate concentration ( Risa Vaka et al., 2019 ; Zhang et al., 2024 ). Plant Material and Growth Conditions Arabidopsis Columbia 0 (Col-0) ecotype were grown in substrate for this study. Seeds were surface sterilized with 95% ethanol followed by a solution containing 20% commercial bleach and 0.1% Tween 20 (VWR, MFCD00165986). Seeds were rinsed 2-3 times with sterile diH 2 O and then stored at 4°C for 4 days in the dark. Seeds were then plated onto Arabidopsis Growth Media (AGM) containing 0.5 x MS with MES (Murashige & Skoog, 1962, RPI, M70300), 1% sucrose and 4g/L Gelrite (RPI, G35020). Plates were incubated vertically in a growth chamber with 120 µmol/m 2 /s PPFD at 22°C with a 16 h/8 h day/night cycle to promote germination. After transfer to potting substrate, plants were grown on controlled growing benches with LED grow lights under similar controlled conditions as plated plants. PPFD was130 µmol/m 2 /s at plant height. Plants were rotated to new positions regularly on grow benches to reduce the impact of uncontrolled environmental effects. Control solutions were prepared in diH 2 O as 4.8 mM potassium nitrate (KNO 3 - ) (Caisson Labs, P012) which matched the concentrations of NO 3 - of the PAW. PAW treatments in substrate were achieved by irrigation of nutrient solutions as follows. A substrate mixture devoid of N was made to avoid any unspecified fertilizer normally present in commercial soil mixes. The substrate mixture contained 45 % peat moss (Premier Peat Moss), 35 % vermiculite (Sta-Green Vermiculite), and 20 % perlite (Aero Soil Perlite) (all measured by volume). Pulverized limestone (Gardenlime Pulverized Dolomitic Limestone) was added to adjust pH to ∼6.0. The substrate was moistened with deionized H 2 O and distributed into 2-inch insert pots (T.O. Plastics, 2401 Standard). Three-day old seedlings previously germinated on sterile AGM media were transferred to each pot of moistened substrate. Pots were incubated at ∼22°C under LED grow lights yielding ∼130 µmol m -2 s -1 in a 16-hour day cycle. Seedlings were thinned to 1 per pot 3 days after transfer. Seedlings were watered with 50ml per pot diH 2 O twice weekly to keep the plants hydrated, and 50ml per pot of 0.25x Hoagland Solution without N (Bio-World, 30630038) was given to all seedlings biweekly by top irrigation. Specific treatments were provided by top irrigation with 50 ml per pot of either PAW or an equivalent NO 3 - control solution once per week. After 5 weeks of growth, adult Arabidopsis plants were then harvested from the substrate. Tomato seeds (Burpee, “Big Daddy Hybrid” 69255A) were directly sown to the substrate mix as described above. Two seeds were sown per pot, and excess seedlings were thinned 1 week after sowing. Seedlings were grown for 5 weeks in a growth chamber at 24°C for a 17-hour day and at 16°C for the night under fluorescent grow lights (GE 46761 54W, 417 umol m -2 s -1 ). Pots were watered every two days with diH 2 O with increasing volume as needed to maintain consistent substrate moisture. Biweekly, 0.25x Hoagland Solution without N (Bio-World, 30630038) was applied to all pots. Seedlings were treated with either PAW (6.5mM; 400 mg/L NO 3 - ) or NO 3 - control solution (6.5mM; 400 mg/L NO 3 - ) starting from week 1. Seedlings were harvested after 5 weeks of growth. Rhizosphere Microbiome Analysis Ten plants were chosen randomly from each treatment, PAW or NO 3 - control, at the end of 5 weeks. Roots were removed from bulk substrate and lightly shaken to remove substrate that was not closely adhered to the root. Then, portions of the remaining substrate were carefully removed with sterile forceps and weighed for harvest. Substrate samples were taken from each individual plant and were not pooled. Bacterial DNA was isolated from approximately 500 mg of substrate sample per plant using the NucleoSpin Soil kit (Takara Bio, 740780). Bacterial 16S rDNA amplicon sequencing was obtained with an Illumina MiSeq (Mr. DNA Lab) using the 515f (Parada) and 806r (Apprill) primers ( Apprill et al., 2015 ; Parada et al., 2016 ; Walters et al., 2015 ). Approximately 50,000 reads were per sample were obtained. Data analysis and processing was all conducted using the R programming language (R-Project). FASTQ files were processed with the DADA2 pipeline ( Callahan et al., 2016 ). Each sample was filtered and trimmed to improve the overall quality of reads. Error-learning, paired-end merging, and chimera removal steps were conducted to maintain quality and accuracy in resulting amplicon sequence variants (ASV) ( Callahan et al., 2016 ). ASVs were further analyzed utilizing the taxonomic tools of the Phyloseq R package ( McMurdie & Holmes, 2013 ) to assign taxonomical IDs to each ASV and calculate both Shannon and Simpson statistics for alpha diversity calculations ( Hein et al., 2008 ; Shannon, 1948 ). Kruskal-Wallis tests were performed to make pairwise comparisons of both Shannon and Simpson statistics. We visualized all data utilizing the ggplot2 package in R. The Bray-Curtis dissimilarity statistics ( Bray & Curtis, 1957 ) were calculated utilizing the developed ASVs. The resulting Bray-Curtis distance matrix was plotted utilizing the Non-metric MultiDimensional Scaling (NMDS) technique for simple visualization as well as a Principal Coordinate Analysis (PCoA), both utilizing ggplot2 package for R. An RRPP analysis of the distance matrix was used for quantitative confirmation of results. Lastly, the taxonomic data attributed to the ASVs was processed through the Phyloseq package ( McMurdie & Holmes, 2013 ), and the top 50 most abundant taxa at the genus level in each given sample were found. These taxa were plotted using ggplot2 to visualize the results. 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