Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis

Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis | 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 Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis T. Scott Carlew , Annika A. Atherton , Ashley Shim , Camilo Parada Rojas , Riley A. Buchanan , View ORCID Profile Jeff H. Chang , View ORCID Profile Joel L. Sachs , View ORCID Profile Brittany J. Belin doi: https://doi.org/10.1101/2025.11.05.682141 T. Scott Carlew 1 Department of Embryology, Carnegie Science , Baltimore, MD 21218 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Annika A. Atherton 1 Department of Embryology, Carnegie Science , Baltimore, MD 21218 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Ashley Shim 1 Department of Embryology, Carnegie Science , Baltimore, MD 21218 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Camilo Parada Rojas 3 Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR 97331 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Riley A. Buchanan 3 Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR 97331 Find this author on Google Scholar Find this author on PubMed Search for this author on this site Jeff H. Chang 3 Department of Botany and Plant Pathology, Oregon State University , Corvallis, OR 97331 Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Jeff H. Chang Joel L. Sachs 4 Department of Ecology , Evolution, and Organismal Biology, UC Riverside, Riverside, CA 92521 Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Joel L. Sachs Brittany J. Belin 1 Department of Embryology, Carnegie Science , Baltimore, MD 21218 2 Department of Biology, Johns Hopkins University , Baltimore, MD 21218 Find this author on Google Scholar Find this author on PubMed Search for this author on this site ORCID record for Brittany J. Belin For correspondence: belin{at}carnegiescience.edu Abstract Full Text Info/History Metrics Supplementary material Preview PDF SUMMARY The paradigms of legume-rhizobia symbiosis are derived primarily from conserved features of Inverted- Repeat Lacking Clade (IRLC) legumes and closely related species. The Dalbergioids diverged from the IRLC early in legume evolution and possess unique symbiotic features but few genetically tractable models. The small, diploid Dalbergioid Aeschynomene americana (American jointvetch) has promise as a genetic model for Dalbergioid-rhizobia symbiosis, yet only a few studies have examined its symbiotic properties. We examined the symbiont range of A. americana from central Florida and characterized a native A. americana nodule isolate, Bradyrhizobium sp. USDA3516. We find that A. americana forms effective symbioses with B. sp. USDA3516, which is closely related to Thai A. americana symbiont B. sp DOA9, and with symbionts from the Dalbergioids stylo and peanut. Interestingly, several strains that effectively nodulated A. americana exhibited branched bacteroid morphologies, but we found that branching was neither necessary nor sufficient for effective symbiosis. Our study contradicts the prevailing view that bacteroid shape is a major determinant of symbiotic efficiency and presents the A. americana - B. sp. USDA3516 interaction as an optimal model of A. americana symbiosis. INTRODUCTION The Fabaceae or legume family of plants contains nearly 30,000 accepted species (Legume Phylogeny Working Group (LPWG), 2025), and many of these species form mutualistic symbioses with nitrogen-fixing rhizobia. Studies of the legume-rhizobia symbiosis have focused on the Papilionoideae subfamily, which is commonly split into Inverted- R epeat L acking C lade (IRLC) tribes and non-IRLC tribes based on presence of an inverted repeat (IR) region in their plastid genomes ( Wojciechowski et al ., 2004 ). Legume genetic tools first were developed in IRLC and closely related non-IRLC species, and as a result, the paradigms for legume-rhizobia symbiotic mechanisms are derived from conserved features across these clades. According to these paradigms, legume-rhizobia symbiosis is initiated by Nod factors that induce development of infection threads and new meristem tissue in the root cortex. This meristem differentiates into nodule cells that are intracellularly infected by rhizobia, which in turn differentiate into bacteroids through a host-dependent process. In soybean, bacteroid differentiation is minimal and consists of upregulation of nitrogen fixation and metabolite exchange factors ( Pessi et al ., 2007 ). In Medicago and other genera, terminal bacteroid differentiation occurs that includes altered bacteroid morphology and increased endoreduplication. This terminal bacteroid differentiation is driven by host n odule-specific, c ysteine-rich (NCR) peptides ( Guerra-Garcia & Sankari, 2025 ). Dalbergioid legumes such as peanut, the world’s second most important commercial legume by production volume (Nations, 2024), diverged from the IRLC ancestor early in Papilionoideae evolution ( Fig. 1A ). This tribe is known to have unique symbiotic features. Many Dalbergioid legumes do not require Nod factors to initiate symbiosis ( Giraud et al ., 2007 ; Guha et al ., 2022 ), and bacterial infection occurs through cracks in the root epidermis rather than an infection thread ( Bonaldi et al ., 2011 ; Noisangiam et al ., 2012 ; Guha et al ., 2022 ). Terminal differentiation of bacteroids does occur in Dalbergioids and is driven by host-produced peptides, but these peptides generally are longer and more anionic than IRLC NCR peptides ( Czernic et al ., 2015 ; Gully et al ., 2018 ; Raul et al ., 2022 ; Boukherissa et al ., 2025 ). Identifying the molecular mechanisms of these unique symbiotic features of the Dalbergioids is key to understanding legume-rhizobia symbiosis evolution. Download figure Open in new tab Figure 1. Selected tribes of the Papillionideae . ( A ) Phylogenetic tree based on conserved regions of matK sequences. Scale bar indicates substitutions per 1000 nucleotides. ( B ) Geographic distribution of Aeschynomene americana (Legume Data Portal, Accessed Sept. 2025). Most genetic work in the Dalbergioids has been performed in the jointvetches ( Aeschynomene spp.), a genus of semi-aquatic legumes that includes the species A. afraspera , A. indica , A. evenia , and A. americana . Of these, only the diploid species A. evenia has a fully assembled genome ( Quilbé et al ., 2021 ). A. americana is also diploid and thus a promising alternative model for Dalbergioid genetics ( Chaintreuil et al ., 2016 ; Brottier et al ., 2018 ), and it has commercial relevance as a cover crop and for rice paddy intercropping ( Fig. 1B ). Currently there are few studies on A. americana symbiosis. Prior work indicates that A. americana symbioses are infection thread-independent and that compatible symbionts (namely Bradyrhizobium sp. DOA9) encode genes for Nod factor production, are non- photosynthetic, and do not terminally differentiate ( Noisangiam et al ., 2012 ; Teamtisong et al ., 2014 ; Okazaki et al ., 2015 ). Here, we examine the symbiotic compatibility of A. americana with a panel of rhizobium type strains, including the A. americana nodule isolate B. sp. USDA3516 ( Grant & Trese, 1996 ). We affirm that A. americana is not compatible with photosynthetic Bradyrhizobium spp. and that its overall symbiont range is more like the Dalbergioids peanut and stylo. Contradicting earlier work, we do observe hallmarks of terminal bacteroid differentiation, including endoreduplication and altered bacteroid morphology; however, altered morphology was not observed in all productive strains. Sequencing of B. sp. USDA3516, the most effective strain tested, indicates that this strain likely produces Nod factors and encodes the BclA protein involved in NCR import ( Guefrachi et al ., 2015 ). These findings suggest that production of NCRs to induce terminal bacteroid differentiation may be universal in the Dalbergioids and is thus an ancient symbiotic mechanism. RESULTS A. americana symbiont range Previous work indicated that A. americana nodulation is Nod factor-dependent and that A. americana is not nodulated with photosynthetic Bradyrhizobium spp. ( Noisangiam et al ., 2012 ). To investigate its symbiont range more broadly, we inoculated A. americana from central Florida with a collection of 13 rhizobium type strains, as well as one native strain ( B. sp. 3516) that isolated from root nodules of A. americana grown in the same region (full strain names are provided in Table 1 ). The type strains used included strains engaged in both Nod factor-dependent and Nod factor-independent symbiosis from diverse hosts. View this table: View inline View popup Download powerpoint Table 1. Strains of rhizobia used for A. americana inoculation . ‘ T ’ indicates type strains. ‘***’ indicates strain was natively isolated from A. americana . At 14 days post-inoculation, we quantified shoot height, nodule counts, nodule dry biomass, and acetylene reduction rates of plants inoculated with each strain ( Fig. 2 ). Four strains provided robust benefits to A. americana , eliciting >10 nodules per plant on average, and had significantly higher nitrogenase activity than uninoculated control plants, including B. stylosanthis , B. arachidis , B. sp. USDA3516, and B. cajani . One strain, Sinorhizobium fredii HH103, provided significant fixed nitrogen but formed relatively few nodules. B. diazoefficiens inoculation increased plant shoot heights but produced few, ineffective nodules, suggesting that the benefit is not strictly due to symbiotic nitrogen fixation. Download figure Open in new tab Figure 2. A. americana growth is promoted by non-photosynthetic Dalbergioid symbionts. Shoot height, nodule number, and nodule dry weight, and acetylene reduction activity for plants inoculated with each strain from Table 1 . NI = ‘Non-Inoculated’ control. N=7-9 plants per condition. Error bars indicate standard deviation. Colors of bars indicate native host tribe, according to the legend in Figure 1 . Asterisks indicate p-values from two-tailed t-test comparison with non-inoculated plants: ‘*’ < 0.01, ‘**’ < 0.001, ‘***’, < 0.0001. None of the remaining strains conferred benefits to A. americana . B. canariense nodulated A. americana robustly, but these nodules did not fix significant nitrogen. B. semiaridum , S. fredii NGR234, and B. brasilense nodulated weakly but also were ineffective. None of the remaining strains formed nodules on A. americana, including B. sp. ORS285, B. BTAi1, B. japonicum , and B. elkanii . A. americana nodule and bacteroid morphology We next examined nodule morphology from A. americana inoculated with each strain that exhibited robust nodulation (at least 10 nodules/plant on average), including B. stylosanthis , B. arachidis , B. sp. USDA3516, B. cajani , and B. canariense . We collected semi-thin sections of nodules harvested at 14 days post inoculation (dpi), stained with Calcofluor and the BacLight LIVE/DEAD kit, and imaged by confocal microscopy. Interestingly, bacteroids of all strains except for B. cajani appeared to have morphological changes relative to typical free-living Bradyrhizobium spp. ( Fig. 3 ). Nodules containing B. sp. USDA3516 had much larger bacteroid volumes and branched bacteroid morphologies, whereas more subtle bacteroid morphological changes occurred in nodules with B. stylosanthis , B. arachidis , and the inefficient fixer B. canariense . We initially hypothesized that the variation in presence of morphological changes in bacteroids across strains was due to some strains requiring longer time windows to complete differentiation. However, nodules harvested at 35 dpi had similar bacteroid morphologies to the 14-dpi time point ( Fig. S1 ). Download figure Open in new tab Figure 3. A. americana bacteroids are terminally differentiated. Representative confocal images of nodule cross- sections collected at 14 dpi. Sections were stained with Calcofluor (cyan), SYTO9 (yellow), and propidium iodide (“PI”; magenta). Scale bars = 10 microns. To obtain more quantitative information on bacteroid characteristics, we isolated bacteroids from root nodules and compared them to free-living cells by imaging and flow cytometry ( Fig. 4 ; Fig. S2-S6 ). In all strains, free-living cell morphologies were similar, exhibiting rod shapes of 3-6 micron length and 1-2 SYTO9 (DNA) foci in the cytoplasmic interior. Staining with the Nile Red (NR) dye under PHB granule-detecting conditions demonstrated that the free-living cells usually had few or no PHB granules. Bacteroid morphologies, however, were diverse across strains. In native symbiont B. sp. USDA3516 ( Fig. 4A ; Fig. S2 ), extracted bacteroids had a branched morphology and were slightly wider than free-living cells. Most bacteroids had multiple PHB granules and SYTO9 was either strong throughout the cytoplasm or present in multiple bright, discrete foci at the poles. The increased volume of B. sp. USDA3516 bacteroids was clear by forward scatter flow cytometry, and SYTO9 flow cytometry indicated that bacteroids had a higher ploidy than free-living cells, with a ∼20% increase in median SYTO9 fluorescence. Bacteroids of B. stylosanthis were similar in properties to B. sp. USDA3516, albeit with a slightly higher increase (40%) in median SYTO9 signal ( Fig. 4D ; Fig. S6 ). We verified that the apparent branched morphologies and larger areas of B. stylosanthis and B. sp. USDA3516 bacteroids were not due to clumping of multiple cells with the membrane dye FM 4-64, which revealed that branched bacteroids were surrounded by one continuous cell envelope ( Fig. S7-8 ). Download figure Open in new tab Figure 4. Productive bacteroids exhibit higher levels of endoreduplication. Representative phase and fluorescence images ( left ) with flow cytometry forward scatter distributions ( center) and SYTO9 intensity distributions ( right ) for bacteroids (“B”, dotted blue filled lines) versus cultured cells (“LC”, solid orange filled line) after staining with Nile Red (NR) and SYTO9: ( A ) B. sp. USDA3516, ( B ) B. arachidis , ( C ) B. cajani , ( D ) B. canariense , ( E ) B. stylosanthis . Scale bars indicate 1 micron. Differentiation of other strains was more variable. B. arachidis also formed mostly branched bacteroids with increased SYTO9 signals relative to free-living cells but contained less pronounced PHB granule staining than in B. stylosanthis and B. sp. USDA3516 ( Fig. 4B ; Fig. S3 ). Bacteroids of B. cajani were slightly larger and wider than free- living cells but were unbranched, and SYTO9 intensity relative to free-living cells was higher than in B. sp. USDA3516 ( Fig. 4C ; Fig. S4 ). Interestingly, bacteroids of B. canariense – the only ineffective symbiont to robustly form nodules – generally were branched and very slightly larger than free-living cells, but these bacteroids had no increase in ploidy. This suggests that endoreduplication rather than branching is the most important aspect of the differentiation, at least within our strain set. Bradyrhizobium sp. USDA 3516 genome properties The apparent terminal differentiation of B. sp. USDA3516 in A. americana was surprising, given that terminal differentiation was not observed in the effective Thai A. americana isolate B. sp. DOA9 ( Teamtisong et al ., 2014 ). To investigate whether this difference could be explained by the gene content of the two strains, we sequenced and assembled the B. sp. USDA3516 genome. We found that the B. sp. USDA3516 genome contains a single 7.8 Mbp chromosome with 7,283 ORFs predicted by both Prokka and Bakta prokaryotic annotation tools ( Fig. 5 ). We did not detect any native plasmids in this strain; commonly Bradyrhizobium spp. do not encode symbiotic plasmids ( Weisberg, A et al ., 2022 ). Download figure Open in new tab Figure 5. Genome architecture of native A. americana symbiont B. sp. USDA3516. Genome architecture of B. sp. USDA3516 consisting of a single circular chromosome. Inner ring (alternating grey regions) denotes individual scaffolds; second rings from center indicate positions of protein-coding genes (CDS, in black) as annotated in Table S1. Outermost rings from center indicate ORFs for symbiotically relevant gene categories, as denoted in the legend. Illustration generated using Proksee ( https://proksee.ca/) (Grant et al. , 2023). We annotated ORFs using the consensus from Bakta ( Schwengers et al ., 2021 ) and Prokka ( Seemann, 2014 ) annotation tools, InterPro protein domain analysis (for protein-coding ORFs) ( Jones et al ., 2014 ), and reciprocal best BLAST hit analysis against closely related and model bacterial strains (list in Methods; Table S1 ). These revealed the presence of well-known symbiosis-driving genes, including nod genes, indicating that this strain can produce Nod factors ( Fig. 5 ). The strain appears to be metabolically versatile with multiple respiratory terminal electron acceptors ( fix /cbb3, cox /c1, and two cyo/ bo3 operons), and though it contains a RuBisCo ( cbb ) gene cluster, it does not contain other genes for photosynthesis in bradyrhizobia ( Mornico et al ., 2012 ). It includes at least three secretion systems ( gsp /T2SS, rhc /T3SS, trb /T4SS) and pili biosynthesis genes ( ctp / tad ), as well as two large flagellar gene clusters ( fla ) and three chemotaxis operons ( che ). Based on synteny with other Rhizobiales, we predict that flagellar cluster fla2 encodes lateral flagellar genes ( Garrido-Sanz et al ., 2019 ). This organism also includes signature lipid species of Bradyrhizobium spp. and rhizobia, such as genes involved in the biosynthesis of hopanoid lipids ( hpn ) and the synthesis and addition of very long chain fatty acids to lipid A ( acpXL ). Comparison of B. sp. USDA 3516 to other symbiotic Bradyrhizobium spp We next assembled a genome-wide phylogeny of Bradyrhizobium species representatives using bac120 alignments from the GTDB Toolkit ( Fig. 6 ) ( Chaumeil et al ., 2022 ). As expected from the gene content, B. sp. USDA3516 is not part of the clade containing photosynthetic bradyrhizobia or the B. japonicum clade, and instead it is more closely related to other productive A. americana symbionts from this study: B. cajani , B. arachidis , and B. stylosanthis . The strain’s closest relatives are B. yuanmingense CCBAU 10071 and the Thai A. americana symbiont B. sp. DOA9, with which it shares >92% average nucleotide identity ( Fig. S9A ). Download figure Open in new tab Figure 6. Bac120 species tree of representative Bradyrhizobium spp. Maximum likelihood tree for conserved regions across select Bradyrhizobium species representative. Branch names for species used for A. americana inoculation in this study are highlighted in purple, and the B. sp. USDA3516 genome is indicated with a black star. Colored boxes at branch tips indicate the legume clade (tribe/subfamily) of the host species from which the strain was originally isolated (see Legend). Numbers at internal nodes (highlighted in white) indicate branch support values using ultrafast bootstrap approximation (UFBoot), based on 1000 bootstraps: 100 = highest confidence, 0 = no confidence. The outgroup sequence is indicated with a grey branch tip label. Scale bar indicates substitutions per 1000 nucleotides. The degree of nucleotide conservation between B. sp. DOA9 and B. sp. USDA3516 is surprising given their contrasting symbiotic phenotypes regarding bacteroid differentiation. We initially hypothesized that they may have lower than average similarity within genes known to be involved in the differentiation process. However, protein phylogenetic trees of the NCR peptide importer BclA (the Bradyrhizbium spp. homolog of BacA in S. meliloti ) ( Guefrachi et al ., 2015 ) indicated that B. sp. USDA3516 BclA is more similar to the B. sp. DOA9 BclA than to the BclA proteins from other species with branched A. americana bacteroids ( Fig. S9B ). We also analyzed the FtsZ protein in B. sp USDA3516, based on recent data demonstrating that FtsZ depletion in the Rhizobiales/Hyphomicrobiales is sufficient to induce branching ( Aubry et al ., 2025 ), yet the FtsZ protein tree topology is likewise similar to the species relationships ( Fig. S9C ). One distinction between B. sp. DOA9 and B. sp. USDA3516 that is not captured by comparing conserved genomic loci is the presence of unique gene groups, and it is possible that bacteroid branching in B. sp. USDA3516 is driven by genes that are not present in B. sp. DOA9. We used the Proteinortho tool ( Klemm et al ., 2023 ) to identify orthologous gene groups (OGs) found in all species with branched bacteroids ( B. sp. USDA3516, B. arachidis , B. stylosanthis , and B. canariense ) and in none of the non-branching species ( B. sp. DOA9 and B. cajani ) ( Fig. S9D ). This analysis yielded a list of 45 OGs ( Table 2 ), which includes genes involved in LPS biosynthesis and DNA replication. Interestingly, seven of these OGs are part of a conserved gene cluster in that is adjacent to the MinCDE cell topology factors ( Fig. 7 ). Though the Min system is not essential in rhizobia, misregulation of Min protein expression in S. meliloti can induce branching ( Cheng et al ., 2007 ), potentially indicating that altered regulation of the MinCDE region is required for branched bacteroids. Download figure Open in new tab Figure 7. Conserved operon adjacent to minCDE in species with branched A. americana bacteroids. Illustration generated using Proksee ( https://proksee.ca/) (Grant e t al. , 2023). View this table: View inline View popup Download powerpoint Table 2. Orthologous gene groups (OGs) specific to species with branched bacteroids in A. americana . OGs identified in all species with branched bacteroids ( B. sp. USDA3516, B. arachidis , B. stylosanthis , and B. canariense ) and in none of the non-branching species ( B. sp. DOA9 and B. cajani ). OGs in bold indicate a conserved operon. MATERIALS & METHODS Bacterial strain cultivation Strain Bradyrhizobium sp. USDA3516 was obtained from the USDA ARS National Rhizobium Germplasm Collection, courtesy of Patrick Elia. Bradyrhizobium spp. ORS285 and BTAi1 were originally obtained from Eric Giraud (LSTM, Montpellier, France) and later gifted by Dianne Newman (Caltech). All other strains were purchased from the DSMZ-German Collection of Microorganisms and Cell Cultures. All Bradyrhizobium spp. and Sinorhizobium spp. strains were streaked on rich AG medium agar plates (4.6 mM sodium gluconate, 6.6 mM arabinose, 1 g/L yeast extract, 6 mM NH4Cl, 5.6 mM MES, 5 mM HEPES, 1 mM Na2HPO4, 1.76 mM Na2SO4, 88 µM CaCl2, 25 µM FeCl3, and 0.73 mM MgSO4, pH 6.6) from 10% glycerol stocks. Plates were grown at 30℃ for 4-5 days before colonies were inoculated into 10mL AG rich liquid media. These cultures were grown to exponential phase (OD 600 = 0.4-0.8) at 30℃ and 250 rpm prior to plant inoculation. For plant inoculation, cultures were pelleted by centrifugation at 4000g in a spinning bucket centrifuge and resuspended to OD 600 = 1.0 in fresh AG. During inoculation, 300 uL of OD 600 = 1.0 resuspensions were added to each 30 mL A. americana culture tube. A. americana cultivation Aeschynomene americana seeds (Hancock Farm & Seed Company) were surface sterilized by a 5-minute incubation in 95% ethanol, followed by 30-minute incubation with 10% bleach, followed by 5 washes in sterile water. The seeds were then plated on 1% water agar plates. Plates were sealed with parafilm, wrapped to prevent light exposure, and germinated at 30℃ for 3 days. Germinated seedlings were rooted into 30 mL culture tubes filled with Bradyrhizobium Nodulation Medium (BNM). Rooted A. americana were then moved to growth chambers held at 12h light/dark cycles at 30℃ and 80% humidity for the duration of the experiment. Acetylene reduction assays Whole A. americana plants were moved into 30 mL Balch tubes with 1mL of sterile water. Balch tubes were plugged with rubber septa and sealed with aluminum crimp caps, after which 10% of the headspace was removed via syringe and 16G needle and replaced with acetylene gas (Airgas). Samples were incubated overnight under growing conditions before measurement of ethylene production by GC-MS as described ( Pan et al ., 2024 ). Bacteroid extraction Nodules were removed from roots and submerged in a 10% bleach solution for 5 minutes. Nodules were then washed three times with Bacteroid Extraction Buffer (BEB) (113.7mM Disodium Malate, 125 mM KCl, 50mM TES buffer) before homogenization with mortar and pestle in 5 mL of BEB. Samples were then centrifuged at 100g for 10 minutes to remove plant debris. Cleared supernatant was moved to a new tube, centrifuged at 1500 g for 20 minutes, and resuspended in 1 mL of ice-cold BEB. All subsequent steps were performed at 4°C with ice-cold buffers. The resuspension was gently added to the top of a freshly prepared Percoll gradient with 10 mL 85%/10 mL 60%/10 mL 45% Percoll layers. The sample was spun through the Percoll gradients 10,000g for 30 minutes, after which a band of concentrated bacteroids was visible. A 5 mL fraction containing this band was collected, diluted 1:10 in BEB, and then centrifuged at 1500g for 20 min. The bacteroid pellet was washed again in 5 mL BEB to remove residual Percoll, resuspended in PBS with 4% fresh paraformaldehyde, and fixed at 4°C overnight. Fluorescence staining Nodule semi-thin sections (100 µm thickness) were collected using a 7000 smz-2 vibratome (Campden Instruments). Nodule sections were stained and mounted for imaging as described ( Pan et al ., 2024 ). For cultured samples, cells were grown to mid-exponential phase (OD 600 = 0.6) and pelleted at 4000 x g for 30 minutes. Cell pellets were resuspended in PBS with 4% fresh paraformaldehyde and fixed at 4°C overnight. Fixed cultured cells and fixed bacteroids prepared as above were stained for microscopy by incubating with 7.5 μM SYTO9 for 30 minutes then with 0.25 μg/mL FM 4-64 for 10 minutes or with 0.5 μg/mL Nile Red for 30 minutes, all in PBS. Microscopy Confocal fluorescence images of nodule cross-sections were taken using a Zeiss LSM980 confocal microscope using either a 40X/1.3 NA or 63X/1.4 NA objective. All images were collected using an Airyscan 2 detector with the following wavelength ranges for each dye: Calcofluor White, 405nm laser excitation and 422-477 nm emission; SYTO9, 488 nm excitation and 495-550 nm emission; Propidium Iodide, 561nm excitation and 607-735 nm emission. For imaging bacteroids, SYTO9 and FM 4-64 fluorescence images were acquired using a Zeiss LSM980 confocal microscope with a 40X/1.3 NA objective. Images were collected using an Airyscan 2 detector with the following wavelength ranges for each dye: SYTO9, 488 nm excitation and 483-506 nm emission; FM 4-64, 514 nm excitation and 500-751 nm emission. Phase images with SYTO9 and Nile Red fluorescence were acquired using a Nikon Ti2 inverted epifluorescence microscope with a 40X/0.75 NA phase objective. The following wavelength ranges were used for each dye: SYTO9 – 488 nm excitation, GFP emission filter cube (502-538 nm); Nile Red – 561 nm excitation, Nikon TRITC emission cube (570-613 nm). Flow cytometry Cultured cells and bacteroids were prepared as described above, stained with 0.025 μM SYTO9 for 15 minutes in PBS, and fixed in 4% paraformaldehyde/PBS at 4°C overnight. Samples were washed three times in PBS and then diluted to 1:10 - 1:100 in 1 mL PBS, depending upon the sample density. Flow cytometry was performed on samples with an Attune Nxt Acoustic Focusing Cytometer rujning Attune Nxt Software v. 3.2.1526.0. Forward scattering was collected at 350V and SYTO9 intensities were collected at 450V using a 488 nm excitation and 500-560 nm emission filter. For each sample, 100,000 events were recorded. Analysis was performed using the FloJo software. Genome sequencing and assembly A. B. sp. USDA3516 was grown at 29°C overnight in a modified arabinose-gluconate medium ( Sachs et al ., 2009 ) with shaking. DNA was extracted from B. sp. USDA3516 and prepared for Oxford Nanopore sequencing, following protocols previously described, with the exception that the Ligation Sequencing Kit V14 was used ( Weisberg, AJ et al ., 2022 ). The PathogenSurveillance pipeline was used to automatically process and assemble reads, assess assembly quality, and annotate the genome sequence ( Foster et al ., 2025 ). Manual genome analysis Preliminary annotation of the B. sp. USDA3516 genome was performed using Prokka version 1.14.5 ( https://github.com/tseemann/prokka ) ( Seemann, 2014 ) and Bakta version 1.11.4 ( https://github.com/oschwengers/bakta ) ( Schwengers et al ., 2021 ). Protein-coding genes were annotated using the InterProScan command line tool (version 5.69-101.0, https://github.com/ebi-pf-team/interproscan ) ( Jones et al ., 2014 ). Genes homologous with selected reference genomes were identified through custom reciprocal best BLAST hit analysis scripts using blastp ( https://www.ncbi.nlm.nih.gov/books/NBK279690/ ) with an e-value threshold of 1e-20. Reference genomes selected for this analysis were Bradyrhizobium sp. ORS 278 ( https://www.uniprot.org/taxonomy/114615 ), Bradyrhizobium BTAi1 ( https://www.uniprot.org/taxonomy/288000 ), Bradyrhizobium diazoefficiens USDA110 ( https://www.uniprot.org/taxonomy/224911 ), Rhodopseudomonas palustris BAA-98 ( https://www.uniprot.org/taxonomy/258594 ), Sinorhizobium meliloti 1021 ( https://www.uniprot.org/taxonomy/266834 ), Caulobacter vibroides (formerly crescentus ) CB15N ( https://www.uniprot.org/taxonomy/565050 ), Bacillus subtilis 168 ( https://www.uniprot.org/taxonomy/224308 ), Escherichia coli K12 ( https://www.uniprot.org/taxonomy/83333 ). Final gene annotations were made by majority-rule across the above preliminary annotation sources and reviewed manually. Chromosome and operon annotations were visualized using Proksee ( https://proksee.ca/ ) ( Grant et al ., 2023 ). Orthologous protein groups were identified using Proteinortho version 6.3.6 ( https://gitlab.com/paulklemm_PHD/proteinortho ) ( Klemm et al ., 2023 ). The following proteome accessions were used for comparison with B. sp USDA3516: Bradyrhizobium arachidis CCBAU 051107 (UniProt UP000594015), Bradyrhizobium brasilense R5 (UniProt UP001221546), Bradyrhizobium BTAi1 (UniProt UP000000246), Bradyrhizobium cajani 1010 (UniProt UP000449969), Bradyrhizobium canariense BTA-1 (UniProt UP000887172), Bradyrhizobium diazoefficiens USDA110 (UniProt UP000002526), Bradyrhizobium sp. DOA9 (NCBI RefSeq GCF_000617845.2), Bradyrhizobium elkanii USDA 76 (NCBI Assembly GCA_023278185.1), Bradyrhizobium japonicum USDA 6 (UniProt UP000005663), Bradyrhizobium sp. ORS 285 (UniProt UP000196578), Bradyrhizobium semiaridum WSM 1704 (NCBI Assembly GCA_020329505.1), Bradyrhizobium stylosanthis (UniProt UP000319949). Phylogenetic tree reconstruction For the Bradyrhizobium species tree, a bac120 alignment of Bradyrhizobium species representatives from the Genome Taxonomy Database (GTDB) was generated using GTDB Toolkit v2.4.0+ (gtdb-tk, https://github.com/Ecogenomics/GTDBTk ) ( Chaumeil et al ., 2022 ). For protein trees, sequences were aligned using the MUSCLE v. 5.1 sequence alignment program ( https://www.drive5.com/muscle/muscle.html ) ( Edgar, 2004 ). Maximum likelihood trees were generated using IQ-TREE 2 ( https://iqtree.github.io/ ) ( Minh et al ., 2020 ). The optimal nucleotide substitution model for each alignment was determined by ModelFinder ( Kalyaanamoorthy et al ., 2017 ) and 1,000 replicates were used to calculate branch support values using ultrafast bootstrap approximation (UFBoot) ( Hoang et al ., 2017 ). Trees were visualized and annotated using TreeViewer ( https://treeviewer.org/ ) ( Bianchini & Sánchez-Baracaldo, 2024 ). DISCUSSION A. americana is a basal, diploid member of the Dalbergioids with potential use as a genetic model for Nod factor- dependent Dalbergioid symbiosis. Here we evaluated the symbiont range of A. americana from central Florida and characterized a nodule isolate from the same region, B. sp. USDA3516, which appears to be a close relative of the effective Thai A. americana symbiont B. sp DOA9. We find that A. americana is effectively nodulated by diverse non-native Bradyrhizobium strains but is not compatible with non-photosynthetic strains, consistent with earlier work. Microscopy of nodule cross-sections and isolated bacteroids revealed that most of the compatible symbionts of A. americana exhibit hallmarks of terminal bacteroid differentiation (branched morphologies and higher ploidy than cultured cells), albeit to varying degrees across symbiont species. What is the role of morphological changes in bacteroids? Prior studies by Lamouche et al . ( Lamouche et al ., 2019a ; Lamouche et al ., 2019b ) attempted to address this question by inoculating the same set of Bradyrhizobium strains ( Bradyrhizobium sp. ORS285, ORS287, ORS335, and ORS357) onto three jointvetch hosts: two species that induce spherical bacteroids ( A. evenia and A. indica ) and one species with elongated bacteroids ( A. afraspera ). The authors then quantified the benefit conferred to each plant by each symbiont via the increase in plant biomass relative to the nodule biomass – a proxy for the benefit to the host relative to the host’s investment in symbiosis. Using this metric, the two jointvetches inducing spherical bacteroids were consistently observed to receive greater benefits from the same strains than the jointvetch with elongated bacteroids. Based on this, the authors concluded that spherical bacteroids may be inherently more effective than elongated bacteroids. Our study contradicts the view that bacteroid morphology per se is a major determinant of symbiotic efficiency. Within the same host, we identified symbionts with four distinct bacteroid phenotypes: (i) branching only, (ii) elevated ploidy only, (iii) both branching and elevated ploidy, and (iv) neither branching nor elevated ploidy. We found that branching alone was not sufficient for a strain to function as an effective symbiont, whereas elevated ploidy was observed in all effective strains. Though the low number of effective symbionts that we identified does not provide a large sample to suggest that higher bacteroid ploidy is strictly necessary for effective A. americana symbiosis, we can conclude that branched bacteroid morphologies are not required, a conclusion that is also supported by the effective interaction between A. americana and the non-branching bacteroids of B. sp. DOA9 ( Noisangiam et al ., 2012 ). The disagreement between this work and Lamouche et al . has several potential explanations. Our groups employ different metrics for evaluating symbiosis (proportion of non-nodule biomass conferred vs. acetylene reduction), and the significance of bacteroid morphological changes may differ between A. americana and the other jointvetches examined. However, we note that Lamouche et al . rely on comparison across rather than within jointvetch species, and that species-specific differences in symbiotic mechanisms beyond morphological changes may account for the symbiosis efficiencies in spherical bacteroid- vs. elongated bacteroid-producing hosts. Ultimately, a careful examination of bacteroid morphotype relevance will require generating symbiont strains lacking only the factors required for bacteroid branching, which could then be assayed in a single host-symbiont context. Currently we do not know what genetic factors regulate morphological and/or ploidy changes in A. americana bacteroids, nor in those of most other Dalbergioid legumes. A. americana presumably produces NCR peptides, and the presence of branched bacteroids likely relates to the degree of compatibility between A. americana NCRs and the presence or sequence of a symbiont’s cell cycle control factors. Others have found that disruption of the cell division factor FtsZ in species of Hyphomicrobiales/Rhizobiales order is sufficient to induce branched cells in culture ( Aubry et al ., 2025 ), as is overexpression of Min proteins Sinorhizobium meliloti (where Min proteins are non-essential) ( Cheng et al ., 2007 ). It is curious, then, that we identified a minCDE- adjacent operon that is conserved in all A. americana symbionts with branched bacteroids, though the function of these genes – and whether they affect Min protein levels – is unknown. This provides the foundation for future work to determine whether A. americana indeed produces NCR peptides, what these peptides target, and whether the conserved minCDE genomic region is relevant to bacteroid differentiation. COMPETING INTERESTS The authors have no competing interests to declare. AUTHOR CONTRIBUTIONS T.S.C., A.A.A., and A.S. performed A. americana inoculation experiments and bacteroid analyses. J.R.S. sequenced and assembled the B. sp. USDA3516 genome. C.P.R., R.A.B., J.H.C., and B.J.B. analyzed the B. sp. USDA3516 genome. B.J.B. designed the project, acquired funding, and prepared the manuscript. DATA AVAILABIITY Bradyrhizobium sp. USDA3615 genome assembly information is available on NCBI, accession # XXXXXXX . Download figure Open in new tab Figure S1. Representative confocal images of nodule cross-sections collected at 35 dpi. Sections were stained with Calcofluor (cyan), SYTO9 (yellow), and propidium iodide (“PI”; magenta). Scale bars = 10 microns. Download figure Open in new tab Figure S2. Additional phase and fluorescence images for B. sp. USDA3516 bacteroids and cultured cells stained with Nile Red (NR) and SYTO9. Scale bars indicate 1 micron. Download figure Open in new tab Figure S3. Additional phase and fluorescence images for B. arachidis bacteroids and cultured cells stained with Nile Red (NR) and SYTO9. Scale bars indicate 1 micron. Download figure Open in new tab Figure S4. Additional phase and fluorescence images for B. cajani bacteroids and cultured cells stained with Nile Red (NR) and SYTO9. Scale bars indicate 1 micron. Download figure Open in new tab Figure S5. Additional phase and fluorescence images for B. canariense bacteroids and cultured cells stained with Nile Red (NR) and SYTO9. Scale bars indicate 1 micron. Download figure Open in new tab Figure S6. Additional phase and fluorescence images for B. stylosanthis bacteroids and cultured cells stained with Nile Red (NR) and SYTO9. Scale bars indicate 1 micron. Download figure Open in new tab Figure S7. Airyscan superresolution imaging of B. sp. USDA3516 bacteroids and cultured cells stained with FM 4- 64 and SYTO9. Scale bars indicate 1 micron. Download figure Open in new tab Figure S8. Airyscan superresolution imaging of B. stylosanthis bacteroids and cultured cells stained with FM 4-64 and SYTO9. Scale bars indicate 1 micron. Download figure Open in new tab Figure S9. (A) Heatmap of average nucleotide identity across stains used for A. americana inoculation and B. sp. DOA9. Calculated with FastANI v. 1.34 ( https://github.com/ParBLiSS/FastANI ) ( Jain et al ., 2018 ) and visualized with Morpheus ( https://software.broadinstitute.org/morpheus/ ) (B-C) Maximum likelihood phylogenetic tree of BclA (B) and FtsZ (C) homologs from genomes in (A). Numbers at internal nodes (highlighted in white) indicate branch support values using ultrafast bootstrap approximation (UFBoot), based on 1000 bootstraps: 100 = highest confidence, 0 = no confidence. UniProt IDs are provided in parentheses in the branch labels. Outgroup sequences are S. meliloti homologs. Scale bars indicate substitutions per 1000 amino acids. (D) Heatmap illustrating the percentage of orthologous gene groups (OGs) shared between B. sp. 3516 and all other strains in (A). View this table: View inline View popup Table S1. Manually curated gene annotations in B. sp. USDA3516. Information provided in each column follows: (A) Ordered locus ID, (B) Contig, (C-D) Start and stop nucleotide positions, relative to the contig; (E) Coding strand (+ or -); (F) Preferred gene names, where available; (G) Consensus gene description; (H) Prokka suggested gene name; (I) Prokka suggested gene description; (J) Bakta suggested gene name; (K) Bakta suggested gene description; (L) InterPro domains identified by Interproscan, formatted as Domain ID:Domain Name; (M) Gene name of reciprocal best BLAST hit (RBBH) from Bradyrhizobium sp. ORS 278, when present; (N) Gene description of RBBH from Bradyrhizobium sp. ORS 278, when present; (O) Gene name of RBBH from Bradyrhizobium BTAi1, when present; (P) Gene description of RBBH from Bradyrhizobium BTAi1, when present; (Q) Gene name of RBBH from Bradyrhizobium diazoefficiens USDA110, when present; (R) Gene description of RBBH from Bradyrhizobium diazoefficiens USDA110, when present; (S) Gene name of RBBH from Rhodopseudomonas palustris BAA-98, when present; (T) Gene description of RBBH from Rhodopseudomonas palustris BAA-98, when present; (U) Gene name of RBBH from Sinorhizobium meliloti 1021, when present; (V) Gene description of RBBH from Sinorhizobium meliloti 1021, when present; (W) Gene name of RBBH from Caulobacter vibroides (formerly crescentus ) CB15N, when present; (X) Gene description of RBBH from Caulobacter vibroides (formerly crescentus ) CB15N, when present; (Y) Gene name of RBBH from Bacillus subtilis 168, when present; (Z) Gene description of RBBH from Bacillus subtilis 168, when present; (AA) Gene name of RBBH from Escherichia coli K12, when present; (BB) Gene description of RBBH from Escherichia coli K12, when present. ACKNOWLEDGEMENTS Funding for this project was provided by the Carnegie Institution for Science Endowment to B.J.B. Pilot experiments were performed by students in the Marine Biological Laboratory’s Molecular & Cell Biology of Symbiosis course, which is funded by a grant from the Gordon & Betty Moore Foundation. We thank Will Ludington (Johns Hopkins University) for Attune flow cytometry access and members of the Ludington lab for training and technical assistance. Members of the Belin lab provided helpful discussions of the manuscript, and Mahmud Siddiqi (Carnegie) provided technical assistance for microscopy. We are grateful to Carnegie Embryology’s IT, front office, and facilities support staff for making our work possible. Funder Information Declared Carnegie Institution for Science, https://ror.org/04jr01610 REFERENCES 1. ↵ Aubry B , Randich A , Hudson B , Horton E , Brown PJB . 2025 . 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OpenUrl Abstract / FREE Full Text View the discussion thread. Back to top Previous Next Posted November 05, 2025. Download PDF Supplementary Material Email Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. You are going to email the following Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website. Your Personal Message CAPTCHA This question is for testing whether or not you are a human visitor and to prevent automated spam submissions. Share Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis T. Scott Carlew , Annika A. Atherton , Ashley Shim , Camilo Parada Rojas , Riley A. Buchanan , Jeff H. Chang , Joel L. Sachs , Brittany J. Belin bioRxiv 2025.11.05.682141; doi: https://doi.org/10.1101/2025.11.05.682141 Share This Article: Copy Citation Tools Aeschynomene americana induces terminal bacteroid differentiation in Bradyrhizobium sp. USDA3516, a novel model for Dalbergioid-rhizobia symbiosis T. Scott Carlew , Annika A. Atherton , Ashley Shim , Camilo Parada Rojas , Riley A. Buchanan , Jeff H. Chang , Joel L. Sachs , Brittany J. 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