Isolation and characterization of a novel strain, Paenibacillus lacisediminis sp. nov., exhibiting both biomacromolecule degradation and plant growth-beneficial activities

Abstract

Background

The Paenibacillus srains exhibit diverse abilities to secrete hydrolases capable of degrading biomacromolecules and to act as plant growth-promoting bacteria (PGPB) through the degradation of fungal cell walls and promotion the nutrient cycling of nitrogen (N) and phosphorus (P). Despite the well-acknowledged attributes of Paenibacillus, only limited studies have identified strains of it concurrently produce multiple hydrolytic enzymes and display strong phytobeneficial characteristics. The objective of this study was to isolate and functionally characterize a novel Paenibacillus strain that combines hydrolytic capabilities with plant growth-promoting potential.

Methods

Strain TH7-28^T was isolated and taxonomically classified through a polyphasic identification approach based on 16S rRNA gene phylogeny, genome analysis, and physiological and biochemical characteristics. Its metabolic capabilities were characterized using CAZy and KEGG pathway annotations, supplemented by Kofam-KOALA functional profiling. Genomic relatedness to reference strains was determined using OGRIs: ANI, dDDH, and tetra-nucleotide frequency signature analyses. Biophysical and biochemical properties were evaluated through enzymatic activity assays, antimicrobial susceptibility testing, respiratory quinone system identification, fatty acid methyl ester profiling, and polar lipid composition analysis. The wheat germination test was used to verify the plant growth-promoting ability.

Results

Strain TH7-28^T was Gram-stain-positive, aerobic, white and rod-shaped. Phylogenetic analysis based on the 16S rRNA gene and genomic sequence indicated that strain TH7-28^T was classified within the genus Paenibacillus. The ANI values of strain TH7-28^T with the closest related strains P. macerans ATCC 8244^T and P. oralis KCOM 3021^T were 91.00% and 92.85%, respectively. The dDDH values of strain TH7-28^T with P. macerans ATCC 8244^T and P. oralis KCOM 3021^T were 44.60% and 52.40%, respectively. The respiratory quinone was menaquinone 7 (MK-7). The major cellular fatty acids (> 10%) comprised anteiso-C_15:0, anteiso-C_17:0, iso-C_16:0 and C_16:0. The genomic DNA G + C content was 52.1%. Phosphatidylethanolamine, two amino lipids and three phospholipids were the main polar lipids. Genomic sequencing revealed multifunctional gene clusters encoding carbohydrate-active enzymes (cellulase and amylase), proteases, and phospholipases, alongside antifungal chitinase and endo-β-1,3-glucanase. The biomolecular metabolic gene types and gene copy numbers of strain TH7-28^T were significantly higher than those of other Paenibacillus genus, indicating its robust capacity for macromolecule degradation. The nitrogen-fixing potential of strain TH7-28^T was confirmed via nifH/D/K genes. Phosphorus activation capacity was demonstrated through pstS/C/A/B-mediated inorganic uptake and phospholipase-driven organic solubilization. Experimental assays further demonstrated significant enzymatic activities of chitinase (8.12 ± 0.66 × 10^–3 U/mL), β-1,3-glucanase (0.023 ± 0.004 U/mL), and nitrogenase (0.164 ± 0.006 U/mL), with concurrent hydrolysis of cellulose, starch, casein, chitin and lecithin. Through the wheat germination experiment, it has been confirmed that this strain significantly enhanced both the seed germination rate and stem length, thereby establishing a solid foundation for subsequent research on its practical applications.

Conclusion

Strain TH7-28^T, isolated from lake sediment, was identified to represent a novel species designated Paenibacillus lacisediminis sp. nov. The strain exhibits multifunctional hydrolase activities, antifungal enzyme synthesis, nitrogen fixation, phosphorus solubilization and plant growth promoting. The findings confirm Paenibacillus lacisediminis sp. nov. as a biotechnologically promising strain for sustainable agriculture, furthermore enriching the functional repertoire of Paenibacillus genus.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-026-04945-5.

Introduction

The genus Paenibacillus was originally proposed by Carol et al. in 1993 [2]. Most members of this genus are Gram-positive, aerobic or facultative anaerobic, rod-shaped and endospore-forming bacteria, with diphosphatidylglycerol as the main polar lipid, MK-7 as the major respiratory quinone, anteiso-C_15:0 as the major cellular fatty acid, and genomic DNA G + C composition from 35 to 59 mol% [53]. At the time of the present writing, there are more than 300 species with validly published and correct names and 8 subspecies of the genus Paenibacillus (LPSN; https://lpsn.dsmz.de/genus/Paenibacillus; [54]). In the past few years, several novel species of the genus were isolated from rhizosphere soil [27, 30], marine [12, 24], forest [37], wetland [44], lake [33, 40], sludge [75], etc.

It has been reported that most Paenibacillus have the capabilities to degrade macromolecules, such as cellulose, starch, casein, and lecithin. The hydrolysis ability varies among different species. P. oralis KCOM 3021 ^T was reported to hydrolyze starch but not casein [53]. P. timonensis CIP 108005 ^T and P. faecis CIP 101062 ^T can hydrolyze starch [9, 61]. P. physcomitrellae DSM 29851^T cannot hydrolyze cellulose, starch, or casein [84]. Paenibacillus sp. PY3 can hydrolyze lecithin but not starch [22]. The hydrolysis of lecithin primarily involves phospholipase, which was divided into different types A1, A2, B, C, and D according to its hydrolyzing positions on phospholipid [4]. P. timonensis LK-DZ15 [76] and P. xylanilyticus W4 [38] are reported to have the capability to produce phospholipase. The hydrolysis of cellulose, starch, and casein mainly depends on the cleavage of the corresponding chemical bonds in macromolecular substrates by cellulase, amylase, and protease [68]. Strains of Paenibacillus genus strains can degrade biomacromolecules by secreting enzyme proteins.

The β−1,3 glucan and chitin are the major components of cell wall of many pathogenic fungi [39]. It has been reported that some Paenibacillus strains can hydrolyze β−1,3-glucan and chitin, such as P. polymyxa KF-1 [81], P. polymyxa HX-100 [83], and P. terrae NK3-4 [82], having β−1,3-glucanase activity. Paenibacillus can destroy the cell wall of pathogenic fungi, thereby inhibiting the growth of pathogenic microorganisms.

Some strains in the genus Paenibacillus can transform unavailable nutrient elements into forms that plants can absorb. For instance, P. polymyxa [20], P. maysiensis [71], P. rhizophilus [60], and P. sabinae [46] have the capability of nitrogen fixation [58]. The above functions enable Paenibacillus to have the potential to promote plant growth. However, Paenibacillus, which can degrade cellulose, starch, casein, and lecithin, and has plant growth-promoting functions, has been rarely reported.

In this study, we successfully isolated a strain that represents a novel species of Paenibacillus. Through the genomic, physiological and biochemical analyses, we elucidated its exceptional capabilities, which encompass degrading macromolecules, inhibiting fungal growth, fixing nitrogen, dissolving phosphorus and promoting plant growth. This research not only expands the strain resource of the Paenibacillus genus but also lays a strong and reliable foundation for forthcoming research on bacteria that promote plant growth.

Materials and methods

Strain isolation and morphology observation

Strain TH7-28^T was isolated from the sediment sample collected in February 2022 from Taihu Lake, PR China (120° 02′ 255"E, 31° 27′ 033"N). The sediments of the lake are characterized by high organic matter, eutrophication and are rich in various functional microorganisms, such as nitrogen cycling microorganisms, carbon metabolism microorganisms, pollutant-degrading microorganisms, and plant growth-promoting microorganisms [67, 77]. The strain TH7-28^T was isolated after incubation at 28 °C for 7 days on modified Reasoner's 2 A (R2A) agar plate [55] using the tenfold dilution series method. The pure culture was stored at −80 °C. The strains were activated with Tryptic Soy Agar (TSA) medium to observe the morphology of colonies and cells. Gram-staining was performed as described previously [18]. The cells were observed by scanning electron microscope (Hitachi Regulus 8100).

16S rRNA gene based identification and phylogeny

Extraction of DNA for molecular analyses was performed by following a rapid alkaline extraction procedure [5]. The 16S rRNA gene was amplified by PCR using the bacterial universal primers E. coli 27F and 1492R [50]. The nearly complete 16S rRNA gene sequence (1450 bp) of strain TH7-28^T was obtained and submitted to GenBank (www.ncbi.nlm.nih.gov) and the EzTaxon server (www.ezbiocloud.net, [79, 80]) to search for similar sequences by using the BLAST algorithm [47]. Phylogenetic trees were created by using the neighbor-joining, maximum-parsimony, and maximum-likelihood methods in MEGA-X software [36]. The Kimura two-parameter method [32] was used for distance calculations, and the resultant tree topologies were evaluated by bootstrap analyses based on randomly generated trees with 1000 replicates [17].

Whole genome sequencing and analysis

Library preparation and sequencing

Strain TH7-28^T was inoculated into the TSB medium and cultured at 37 °C, 150 rpm for 12 h. The cells were collected by centrifugation and washed three times with sterile water. Library construction and Whole Genome Sequencing (WGS) were performed using the sequencing platform of Illumina Novaseq. The concentration of DNA was measured with Quantus Fluorometer (Picogreen). The integrity of DNA was examined by electrophoresis on a 1% agarose gel. The library was constructed using the Illumina platform's Pair End dual-end sequencing method, and the insert fragments of the library were generally 400-500 bp. The library construction quality and sequencing quality of the samples were analyzed using the quality control software Fastp v0.20.0 (https://github.com/OpenGene/fastp). Pre-assembly processing of the generated reads, including quality control and trimming, was conducted using SOAPdenovo2 (http://soap.genomics.org.cn/).

Genome assembly

The optimized sequences obtained from the second-generation sequencing were assembled using the short sequence assembly software Spades v4.0.0 (https://cardgames.io/spades/), with multiple Kmer parameters (kmergenie) for concatenation. The optimal contig assembly results were achieved. Subsequently, the reads were aligned to the contigs. Leveraging the paired-end and overlapping relationships among the reads, local assembly and optimization were carried out on the assembly results to construct scaffolds. To validate the accuracy of the data, BUSCO v5.4.5 (https://busco.ezlab.org/) and CheckM v1.2.1 were employed to assess the quality and completeness of the genome assembly results.

The assembly results by Glimmer (http://ccb.jhu.edu/software/glimmer/index.shtml; [11]) were used to predict the coding genes. The assembled contiguous sequences were then submitted to the NCBI Prokaryotic Genome Annotation Pipeline for gene annotation. The software Circos version 0.66 [35] was used to make the genome circle map and calculate the genome length and the DNA G + C content.

Genome-based taxonomy

To elucidate the precise taxonomic classification of TH7-28^T, its draft genome sequence was meticulously analyzed using a suite of genome-based taxonomic classification tools. The draft genome sequence-based tree was reconstructed using CVTree3 Web Server (http://cvtree.online/v3/cvtree/; [87]) with the K-value setting of 6, and the core gene tree based on the draft genome sequences was inferred with Type (Strain) Genome Server (TYGS; https://tygs.dsmz.de/; [48]). The taxonomic positioning of TH7-28^T was assessed through the computation of overall genome-relatedness indices (OGRIs) in comparison to other Paenibacillus species, utilizing the method as previously reported [51]. The average nucleotide identity (ANI) value was calculated using the online ANI Calculator (http://jspecies.ribohost.com/jspeciesws/, [79, 80]). The digital DNA-DNA hybridization (dDDH) value was determined using the Genome-to-Genome Distance Calculator (GGDC) version 2.1(http://ggdc.dsmz.de/distcalc2.php, [49]). The analysis of gene collinearity among strains was carried out using the collinear website (https://www.bv-brc.org/; [52].

Comparative pangenomic analysis

The pan-genome encapsulates the complete genetic repertoire of a species, encompassing the collective gene pool of all its strains. It is primarily composed of three distinct components: core genes, accessory genes, and strain-specific unique genes. By using the Orthofinder v2.3.3 software (https://github.com/davidemms/OrthoFinder/releases/tag/2.3.7) and employing the blast + mcl clustering approach, a comparative analysis was conducted on the genome of P. lacisediminis TH7-28^T alongside those of P. macerans ATCC 8244^T and P. oralis KCOM 3021^T. Such an in-depth examination aimed to identify both differences and commonalities, thereby further elucidating the taxonomic specificity and functional relevance of P. lacisediminis TH7-28^T.

Functional annotation of genomic sequences

The metabolic and biosynthetic gene repertoire of strain TH7-28^T was functionally annotated using Gene Ontology (GO) terms [3] and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway mapping [28]. To elucidate carbohydrate-active enzymes (CAZymes), the genomic sequences were analyzed against the Carbohydrate-Active EnZymes (CAZy) database (http://www.cazy.org/, [43]). Antimicrobial resistance determinants were identified using the Comprehensive Antibiotic Resistance Database (CARD; [25]), which integrated homology modeling and resistance annotations to predict phenotypic resistance profiles. Whole-genome KEGG Orthology (KO) annotations were performed for strain TH7-28^T and its phylogenetically related taxa using the KofamKOALA web server (https://www.genome.jp/tools/kofamkoala/, [1]). This analytical approach provided pivotal insights by enabling a characterization of macromolecule degradation processes like cellulose, starch, casein, and lecithin breakdown, unveiling plant growth-promoting traits such as indole-3-acetic acid synthesis, and facilitating a comparative assessment of metabolic potential. The ChiPlot web tool (https://www.chiplot.online/) was then utilized for gene cluster visualization, employing hierarchical clustering to organize functionally related genomic regions.

Accession numbers

The 16S rRNA gene sequence of the isolate was submitted to GenBank of the NCBI database with accession number PQ816947. The Whole Genome Shotgun project has also been deposited in the NCBI database under the BioProject number PRJNA1204380 and the genome accession number JBKIAX000000000.

Physiological and chemotaxonomic identification

Cells of strain TH7-28^T grown on TSA at 37 °C for 2–3 days were used for physiological and biochemical tests. Cell growth at various temperatures (4, 10, 15, 20, 28, 30, 37, 40, 45, 45, 50, 60 °C) was evaluated in TSB (Tryptic Soy Broth) broth. The pH range for growth was assessed in TSB broth with pH value adjusted to 3.0–12.0 (at intervals of 0.5 pH unit). The pH of TSB broth was adjusted with the appropriate biological buffers (CH₃COOH/CH₃COONa for pH 3–5.5, Na₂HPO₄/NaH₂PO₄ for pH 6–8, Na₂CO₃/NaHCO₃ for pH 8.5–10, and NaOH/HCl for 10.5–12). The tolerance to NaCl (0–5%, w/v) at intervals of 0.5% was determined in the TSB medium. The abilities to hydrolyze starch, casein, Tween 80 and CM-cellulose were tested as described by Smibert and Krieg [65]. Bubble production in 3% (v/v) H₂O₂ was used to determine the catalase activity. Oxidase activity was determined by using 1% (w/v) N, N-dimethyl-p-phenylenediamine. Urease, H₂S production, indole production, sugar utilization and acid production were evaluated as described by Dong and Cai [15]. Sensitivity of TH7-28^T to the antibiotics, including penicillin (10 U), carbenicillin (100 µg), chloramphenicol (30 µg), neomycin (30 µg), kanamycin (30 µg), streptomycin (10 µg), and tetracycline (30 µg), was detected after incubation for 1 day at 37 °C on TSA medium [29]. The type strains, P. macerans ATCC 8244^T, purchased from American Type Culture Collection (ATCC), were used as the reference.

Cells cultured in TSB broth for 24 h at 37 °C were used for respiratory menaquinones, polar lipids, and cellular fatty acid analysis. Menaquinones were extracted and purified according to the methods of Collins [10] and detected using an HPLC system. Polar lipids were extracted according to the methods of Collins [10] and analyzed by two-dimensional TLC using silica gel 60 plates (Merck, [63]), which were separated using the solvents chloroform–methanol-water (65:25:4, v/v/v) in the first dimension and chloroform–methanol-acetic acid–water (80:18:12:5, v/v/v/v) in the second dimension. Fatty acid methyl esters were prepared and determined by the Sherlock Microbial Identification System (MIDI) according to the manufacturer’s instructions [63]. P. macerans ATCC 8244^T was used as the reference for the aforementioned evaluation.

Determination of degradation ability of macromolecules

To evaluate the starch-degradation capability of strain TH7-28 ^T, it was inoculated into beef extract peptone medium supplemented with 0.2% soluble starch, with the pH adjusted to 7.0. Following incubation at 37 ℃ for 24 to 72 h, the formation of a transparent zone was examined through iodine staining [8].

To assess the cellulose-degradation potential of the strain, it was inoculated into inorganic salt medium containing 1% sodium carboxymethyl cellulose, 0.1% K₂HPO₄, 0.1% KH₂PO₄, 0.02% MgSO₄⋅7H₂O, 0.1% NH₄NO₃, 0.005% FeCl₃⋅6H₂O, 0.002% CaCl₂ and 1.5% gelatin, with pH of 7.0. After being cultured at 37 ℃ for 24 to 72 h, the presence of a transparent zone was detected using the Congo red staining method, as described by Ghalib et al. [19] and Rawway et al. [56].

To determine the lecithin-degrading ability, strain TH7-28 ^T was inoculated onto the Monjina solid medium containing 1% glucose, 0.05% (NH₄)₂SO₄, 0.03% MgSO₄·7H₂O, 0.03% NaCl, 0.03% KCl, 0.003% FeSO₄·7H₂O, 0.003% MnSO₄·4H₂O, 0.5% CaCO₃, 0.1% egg yolk lecithin and 1.5% agar, pH 7.0. After culturing at 37 ℃ for 24 to 72 h, the transparent ring was observed [85].

To detected the casein-degrading capability, strain TH7-28 ^T was inoculated onto the casein medium containing 1% casein, 0.5% yeast extract, 1% NaCl and 1.5% agar, pH 7.0. After culturing at 37 ℃ for 24 to 72 h, the transparent ring was observed [62].

Nitrogenase, chitinase and β−1,3-glucanase activity detection

Strain TH7-28 ^T was inoculated into TSB broth and cultured at 37 ℃ for 24 h. The cells were collected by centrifugation and resuspended in sterile water to OD₆₀₀ of 1.0. The resuspended bacterial suspension was quantitatively inoculated (V/V, 5%) into the Ashby nitrogen-free medium [26], the chitinase fermentation medium [69] and the β−1,3-glucanase fermentation medium [74], respectively, and then cultured at 37 °C, 150 r/min for 5 days. The supernatants were collected for the detection of nitrogenase activity by using the nitrogenase reagent kit (Shanghai Yude Biotechnology Co., Ltd.), chitinase by the chitinase reagent kit (Shanghai Yude Biotechnology Co., Ltd.), and β−1,3-glucanase by the DNS method [74], respectively. The amount of enzyme required to hydrolyze 1 μmol of β-glucan to reducing sugars (measured as glucose) per minute is defined as one unit of β-glucanase activity (U).

Triticum aestivum L. germination and seedling evaluation

The wheat seeds of Triticum aestivum L. Zhengmai 165 with plump and uniform size were soaked in a 1% hypochlorite solution for 10 min for surface disinfection. The sterilized seeds were then thoroughly rinsed with distilled water for several times and air-dried on a sterile gauze sheet [45].

Strain TH7-28^T was used in the wheat seed soaking experiment to verify the plant growth-promoting activity. The cells were activated in TSB broth and suspended in sterile water to a concentration of 1 × 10⁸ CFU/mL. One hundred wheat seeds were immersed in the cell suspension at 28 ℃ for 2 h, and seeds immersed in the sterile water were used as control [6]. Then the seeds were placed on filter paper to dry for 5 min, transferred to moistened gauze with a layer of moistened gauze covering the surface, and placed in a chamber at 28 ℃ for germination. Each processing sets 3 repetitions.

The germination rate of wheat seeds was statistically recorded every day. The rate = Number of germinated seeds/Number of tested seeds × 100% [57]. Randomly 5 seedlings with consistent growth were selected from each replicate to measure the lengths of the shoots.

Results

Morphological characteristics of strain TH7-28^T

Strain Paenibacillus lacisediminis TH7-28^T is preserved at the Marine Culture Collection of China (MCCC, https://www.mccc.org.cn/) with the accession numbers of MCCC 1K09615. Colonies of strain TH7-28^T are white, convex, round, and approximately 1.2-2.5 mm in diameter after cultured on TSA medium for 2 days at 37 °C. Gram stain was observed to be positive. The cells were rod-shaped with 0.2–0.5 µm in width and 1.4–2.4 µm in length (Supplementary Fig. S1, available in the online version of this article).

Phylogenetic results based on the 16S rRNA gene sequences

The 16S rRNA gene sequence was used to investigate the taxonomic status. Similarity analysis indicated that strain TH7-28^T showed the highest 16S rRNA gene sequence similarity to P. oralis KCOM 3021^T (98.2%), followed by P. macerans ATCC 8244^T (98.1%), P. barengoltzii NBRC 101215^T (97.5%), P. horti KACC 19299^T (97.2%), P. rhizolycopersici DXFW5ᵀ (97.2%), and the similarity with other species of the genus Paenibacillus was less than 97%, which are below the recommended species differentiation cutoff of 98.65% [31]. The neighbour-joining tree (Fig. 1) indicated that strain TH7-28^T was clustered in the genus Paenibacillus and formed a robust branch with P. oralis and P. macerans. This phylogenetic topology is confirmed in the maximum-parsimony and maximum-likelihood trees (Supplementary Fig. S2).

Fig. 1.

Neighbour-joining tree, based on 16S rRNA gene sequences, showing the relationship between strain Paenibacillus lacisediminis TH7-28^T with P. macerans ATCC 8244^T, P. oralis KCOM 3021^T, and other closely related strains. Bar, 0.05 substitutions per nucleotide position. Filled circles indicate that the corresponding nodes were also recovered by the maximum-parsimony and maximum-likelihood algorithms. Numbers at nodes are bootstrap percentages > 50% (based on 1000 resamplings). Zobellella aerophila JC2671^T (HM475140) was used as the outgroup

Genome features of TH7-28^T

The total DNA extracted from strain TH7-28^T is 11.47 μg, which meets the requirements for Illumina PE library construction. The quality control data show that the raw Q20 and Q30 values were 98.58% and 93.61%, with clean Q20 and Q30 values of 98.91% and 94.22%, respectively, indicating its good sequencing quality. The assembly results of strain TH7-28^T are shown in Table S1 (available in the supplementary materials), and the assembly evaluation results are presented in Table S2. Results showed that the genome's completeness is 99.85%, the genome's contamination degree is 0, and the genome's strain heterogeneity is 0.

The genome circle map of strain TH7-28^T is shown in Fig. 2. The total genome size of the isolate was 7,279,269 bp, which contained 6281 protein-coding genes, 80 tRNAs, and 5 rRNAs. The genomic G + C content of strain TH7-28^T was 52.1%, which was within the scope of the genus Paenibacillus (35–59%; [70]).

Fig. 2.

The genome circle map of strain TH7-28^T made by the software Circos version 0.66, for which the corresponding information from the outer circle to the inner circle is genome size identification, gene information on positive and negative chains, ncRNA, GC content, and GC-Skew

Phylogenomic features and genome-based taxonomy of TH7-28^T

To further elucidate the phylogenomic placement of strain TH7-28^T, the draft genome was compared to the other related type strains using the CVTree3 Web Server and TYGS database. From the whole-genome phylogenetic tree, strain TH7-28^T was clustered within the genus Paenibacillus. The phylogenetic analysis based on the core gene sequences (Fig. 3) indicated that strain TH7-28^T was different from the other members of Paenibacillus. The Genome size and protein count of strain TH7-28^T were significantly different from those of strain P. oralis KCOM 3021^T.

Fig. 3.

Whole genome-based phylogenetic tree showing the relationship of P. lacisediminis TH7-28^T to its closest relatives (Genbank accession numbers in brackets). Tree inferred with FastME 2.1.6.1 from GBDP distances calculated from genome sequences. The branch lengths are scaled in terms of the GBDP distance formula D5. The numbers above the branches are GBDP pseudo-bootstrap support values > 60% from 100 replications. The tree was rooted at the midpoint

The results of ANI and dDDH analysis were shown in Fig. S4. The ANI comparison results of strain TH7-28^T with P. macerans ATCC 8244^T and P. oralis KCOM 3021^T were 91.00% and 92.85%, respectively, both lower than the accepted species limit of 95% [59]. The dDDH value between strains TH7-28^T and P. macerans ATCC 8244^T (44.60%) and P. oralis KCOM 3021^T (52.40%) was below the 70% cutoff recommended for genomic species identification [72]. These results further distinguished strain TH7-28^T from P. macerans ATCC 8244^T and P. oralis KCOM 3021^T.

The homology analysis results showed that strain TH7-28^T had 158 homologous genomic contigs. In contrast, strain P. oralis KCOM 3021^T had only 4 such contigs, while strain P. macerans ATCC 8244^T had 81. Some homologous genes were in different positions with complicated cross-linking, indicating the differences between the three strains (Fig. 4).

Fig. 4.

Collinearity of strains TH7-28^T, P. macerans ATCC 8244^T, and P. oralis KCOM 3021^T. The analysis of gene collinearity among strains was carried out using the collinear website (https://www.bv-brc.org/). The different colored lines in the figure are the Locally Collinear Block (LCB) connection lines. Each connection line clearly indicates a specific homologous LCB block between two genomes. The two ends of each line are respectively connected to the same LCB located on different genomes. By observing the direction of the LCB connection lines, the arrangement order of LCBs in different genomes can be seen. The homologous gene clusters are distributed relatively randomly among the three, with a scattered arrangement. The LCB connection lines have complex cross-connections, further demonstrating that the three are different strains

By conducting a comparative analysis of the pan-genome of strain TH7-28^T with P. oralis KCOM 3021^T and P. macerans ATCC 8244^T, the results showed that the total gene numbers of strain TH7-28^T, P. oralis KCOM 3021^T, and P. macerans ATCC 8244^T were 6807, 6904, and 6373, respectively, and the core gene numbers were 4737, 4752, and 4727, respectively. The unique gene numbers were 1350, 2152, and 1649, respectively, and the non-essential gene numbers were all 0 (Fig. 5A). It can be seen (Fig. 5C, D) that at the COG classification level in the pangenome, there were significant differences (P < 0.05) in the genes annotated as being associated with metabolism and cellular processes signaling; at the KEGG classification tier, statistically significant differences (P < 0.05) were observed among the genes annotated as being linked to cellular processes, organismal systems, environmental information processing and genetic information processing. By comparing the COG database and KEGG database analysis results (Fig. 5E–H), it was found that there were significant differences in the number of genes annotated in different functional classifications between strain TH7-28^T with P. oralis KCOM 3021^T and P. macerans ATCC 8244^T. Simultaneously, a comparative analysis of the three strains' gene counts related to large molecule degradation and plant growth promotion was conducted. The findings revealed strain TH7-28^T harbored a greater number of functional genes compared to P. oralis KCOM 3021^T and P. macerans ATCC 8244^T, which included those involved in cellulose degradation, fungal inhibition, nitrogen fixation, and phosphorus solubilization (as depicted in Fig. 5I). This finding strongly suggests that strain TH7-28^T possesses a superior capacity for large molecule degradation and plant growth promotion, and further distinguishes the isolate apart from P. oralis KCOM 3021^T and P. macerans ATCC 8244^T in terms of functional classification.

Fig. 5.

Comparative analysis of the whole genomes of strain TH7-28^T, P. macerans ATCC 8244^T and P. oralis KCOM 3021^T. A Pan-genome Venn diagram. The numbers in the crossed sections indicate the number of common homologous genes, while the numbers in the separate sections represent the number of unique homologous genes. B Genetic hierarchical clustering analysis, with the distance algorithm set as "abund_jaccard" and the clustering method set as "average". The left side shows the sample clustering tree, where the branch length represents the distance between samples; the right side shows the distance heatmap, with different colored squares representing the distance between samples, and the numbers within the squares indicating the calculated distance. C COG classification: Core genes and pan-genome difference analysis. D KEGG classification: Core and pan-genome difference analysis. Different numbers of asterisks * indicate significant differences. *, P < 0.05; **, P < 0.01; ***, P < 0.001. E KEGG pathway comparison. F COG category comparison. G COG function comparison. H KEGG enrichment analysis. Enrichment rate, that is, the ratio of the number of enriched genes in the pathway to the number of annotated genes. The higher the ratio, the higher the enrichment degree. I Number of functional genes

Physiologic and chemotaxonomic characteristics of strain TH7-28^T

The growth of strain TH7-28^T occurred at 20–55 °C (optimum, 45 °C), pH 6.0–9.0 (optimum, pH 7.5), and in 0–4.5% (w/v) NaCl (optimum, 1.5%). Strain TH7-28^T was positive for nitrate reduction and indole production, but negative for nitrite reduction, denitrification, and H₂S production. Oxidase and catalase were positive, but urease was negative. Hydrolysis of starch, cellulose, lecithin, casein, and skimmed milk were positive, but hydrolysis of Tween-80 and gelatin were negative. Glycerol, D-mannose, sucrose, D-xylose, xylan, D-raffinose, D-glucose, maltose monohydrate, ribose, D-galactose, mannitol, L-arabinose, L-rhamnose, lactose, and D-fructose could be used as the carbon and energy sources with acid production, but not sorbitol, D-trehalose, ethanol, glycine, adenosine, glutamic acid, aspartate, lysine, or cysteine. Sensitive to kanamycin, ampicillin, chloramphenicol, neomycin, streptomycin and tetracycline, but insensitive to penicillin. The detailed physiological and biochemical characteristics of strain TH7-28^T were given in the description of species. The distinguishing characteristics of strain TH7-28^T from the closely related reference strains were listed in Table 1. Through comparative analysis, it becomes evident that strain TH7-28^T exhibits distinct characteristics in terms of its salt tolerance concentration, pH and temperature ranges for growth, indole production capacity, as well as its abilities to degrade casein and lecithin, and utilize glycerol and sucrose, when compared to its closely related species, namely P. macerans ATCC 8244^T, P. oralis KCOM 3021^T, and P. timonensis CIP 108005^T. These differences provide compelling support for the delineation of strain TH7-28^T as a distinct species.

Table 1.

Different phenotypic characteristics of strain TH7-28^T and the type strains representing the closest related species

Characteristic	1	2	3	4
NaCl range for growth (%, w/v; optimum)	0–4.5 (1.5)	0–5.0 (1.0)	0–4.0 (1.0)	0–3.0 (ND)
pH range for growth (optimum)	6.0–9.0 (7.5)	3.0–9.0 (7.0)	5.5–9.5 (8.0–8.5)	ND
Temperature range for growth (℃; optimum)	20–55 (45)	20–55 (40)	25–45 (35)	30–50 (30–37)
Indole production	+	-	-	ND
Nitrate reduction	+	-	+	w
Oxidase	+	-	-	-
Catalase	+	-	+	+
Hydrolysis of:
Casein	+	-	-	ND
Lecithin	+	-	ND	ND
Antibiotic susceptibility:
Penicillin	-	-	ND	+
Acid production from:
Glycerol	+	-	w	-
Sucrose	+	-	ND	-
D-trehalose	-	-	+	+
D-xylose	+	+	-	+
D-raffinose	+	-	+	-
Ribose	+	+	+	-
Mannitol	+	+	+	-
Genomic DNA G + C (mol %)	52.1	52.5	51.3	54.0

Strains: 1, P. lacisediminis TH7-28^T; 2, P. macerans ATCC 8244^T; 3, P. oralis KCOM 3021^T; 4, P. timonensis CIP 108005^T. Data for strains 1–2 were from this study; and data for strains 3–4 were taken from Park et al. [53] and Roux and Raoult [61], respectively. +, Positive; –, negative; w, weakly positive; ND, no data available

The menaquinone detected in strain TH7-28^T was MK-7, which was consistent with the characteristic of the genus Paenibacillus. Phosphatidyl ethanolamine (PE), two aminolipids (AL), and three phospholipids (PL) were the main polar lipids (Fig. S3). The major fatty acids (> 10%) of strain TH7-28^T were anteiso-C_15:0 (34.54%), anteiso-C_17:0 (19.64%), iso-C_16:0 (14.36%) and C_16:0 (13.22%). Compared with the most closely related P. macerans ATCC 8244^T, the major fatty acids of strain TH7-28^T had lower amounts of C_16:0, higher amounts of anteiso-C_15:0, anteiso-C_17:0 and iso-C_16:0, and the content and composition of the other fatty acids, such as C_14:0 and C_17:0, were also different. The whole fatty acid contents of strain TH7-28^T and its reference strains were list in Table 2.

Table 2.

Cellular fatty acids of strain TH7-28^T and the reference strains

Fatty acids	1	2	3	4
Straight chain:
C14:0	-	1.9	1.2	1.3
C15:0	-	-	-	2.0
C16:0	13.2	19.8	16.6	10.6
C17:0	1.4	-	-	-
C18:0	-	8.4	-	-
Branched chain:
iso-C14:0	1.3	-	1.4	8.2
iso-C15:0	4.6	3.7	4.3	10.1
iso-C16:0	14.4	12.3	14.5	15.5
iso-C17:0	5.17	5.03	4.4	1.9
anteiso-C15:0	34.5	21.3	43.4	43.4
anteiso-C17:0	19.6	15.3	12.4	4.0
Unsaturated:
C18:1ω9c	-	3.7	-	-
Summed Feature 8	-	3.4	-	-

Strains: 1, P. lacisediminis TH7-28^T; 2, P. macerans ATCC 8244^T; 3, P. oralis KCOM 3021^T; 4, P. timonensis CIP 108005^T. Data for strains 1–2 were from this study, and data for strains 3–4 were taken from Park et al. [53] and Roux and Raoult [61], respectively. Fatty acids amounting to more than 10% are highlighted by bold type, and total fatty acids amounting to less than 1% in all strains are not listed. -, < 1% or not detected

Summed features are fatty acids that cannot be resolved reliably from other fatty acids using the chromatographic conditions chosen. The MIDI system groups these fatty acids together as one feature with a single percentage of the total

Summed feature 8 comprised C_18:1 ω7c and/or C_18:1 ω6c

On the basis of the genotypic, phenotypic, biochemical and phylogenetic differences, it is proposed that strain TH7-28^T represents a novel species of the genus Paenibacillus, for which the name Paenibacillus lacisediminis sp. nov. is proposed.

Genomic annotation and functional potential of strain TH7-28^T

Antibiotic resistance and hydrolase

Strain TH7-28^T mainly contained genes to resist antibiotics, including disinfecting agents, glycopeptide antibiotics, lincosamide antibiotics, phosphonic acid antibiotics, and tetracycline antibiotics. The carbohydrate active enzyme annotation information showed that strain TH7-28^T contained 236 glycoside hydrolases (GHs), 61 glycosyl transferases (GTs), 29 carbohydrate esterases (CEs), 5 auxiliary activities (AAs), 10 polysaccharide lyases (PLs), and 82 carbohydrate-binding modules (CBMs). The most abundant GH families were GH13 (n = 24), implicated in starch degradation, and GH43 (n = 22) often involved in hemicellulose decomposition. The presence of multiple enzymes from families AA3 (e.g., alcohol oxidases) and CE4 (acetyl xylan esterase) suggested the potential capacity to modify and degrade complex polysaccharides.

Macromolecules degradation

Through annotation using the KEGG database, the complete genome of strain TH7-28^T was analyzed, leading to the identification of a diverse array of genes associated with biomacromolecule metabolism. Among these, genes related to the metabolism of cellulose, starch, casein, and lecithin emerged as focal points of interest as illustrated in Fig. 6. The gene cbhA (encoding cellulose 1,4-beta-cellobiosidase [EC:3.2.1.91]) is annotated in Scaffold 6, Scaffold 7, Scaffold 18, and Scaffold 21. The gene pulA (encoding pullulanase [EC:3.2.1.41]) is annotated in Scaffold 2, Scaffold 7, Scaffold 8, and Scaffold 23. The gene nplT (encoding neopullulanase [3.2.1.135]) is annotated in Scaffold 3 and Scaffold 23. The gene pqqL (encoding zinc protease [EC:3.4.24.-]) is annotated in Scaffold 14. The gene gpr (encoding spore protease [EC:3.4.24.78]) is annotated in Scaffold 3 and Scaffold 5. The gene gluP (encoding rhomboid protease GluP [EC:3.4.21.105]) is annotated in Scaffold 1. We also identified genes for degrading lignin and pectin in TH7-28^T, including (4-O-methyl)-D-glucuronate-lignin esterase [EC:3.1.1.117] and pectinesterase [EC:3.1.1.11]. The presence of these genes indicates that strain TH7-28^T has the potential to degrade cellulose, starch, pectin, lignin, and casein. In addition, the whole genome analysis revealed that strain TH7-28^T also has a variety of phospholipase enzyme genes, including the genes of N-acyl-phosphatidylethanolamine-hydrolysing phospholipase D [EC: 3.1.4.54], phospholipase D1/2 [EC: 3.1.4.4], cardiolipin-specific phospholipase [EC: 3.1.1.-], lysophospholipase [EC: 3.1.1.5] and phospholipase/carboxylesterase.

Fig. 6.

Genes of hydrolysis of cellulose, starch, casein, and lecithin; and the hydrolysis ability of strain TH7-28^T with the reference strain ATCC 8244^T. It includes a total of 7 genes related to the degradation of macromolecules. Among them, genes pulA, pqqL, gpr, and gluP are related to casein hydrolysis; cbhA is related to cellulose degradation; nplT is related to starch hydrolysis; pldB is related to the hydrolysis of lecithin. The gene clusters are color-coded, with the same gene clusters represented by the same color and different gene clusters displayed in different colors. The transparent zone on the plates showed the hydrolysis ability of the two strains

The annotation of the above genes in the genome of strain TH7-28^T and the comparison results with other species within the genus Paenibacillus are shown in Table S3. The results showed that the macromolecule metabolic genes of strain TH7-28^T were significantly higher than those of the reference strains in terms of gene species and gene copy number. From a genetic perspective, this indicates that strain TH7-28^T may have excellent potential for degrading biological macromolecules in the Paenibacillus genus.

Plant growth promoting function

The β−1,3 glucan and chitin are the main components of cell wall of many pathogenic fungi. Based on the genome annotation results, we found that strain TH7-28^T contained genes encoding endo-1,3 (4) -beta-glucanase [EC: 3.2.1.6] and chitinase [EC: 3.2.1.14] for degrading β−1,3-glucan and chitin, respectively. This indicated that the strain had the potential for an antifungal function.

We analyzed the nitrogen fixation genes in the whole genome of strain TH7-28^T. The results showed the strain had various nitrogen-fixing genes, including gene nifH encoding nitrogenase iron protein NifH, the genes nifD and nifK of nitrogenase molybdenum-iron protein alpha chain [EC: 1.18.6.1], the gene nifE of nitrogenase molybdenum-cofactor synthesis protein NifE, the gene nifN of nitrogenase molybdenum-iron protein NifN, the gene iscU of nitrogen fixation protein NifU and related proteins, the gene nifB of nitrogen fixation protein NifB and the gene nifX of nitrogen fixation protein NifX. The abundant nitrogen-fixation genes indicated that this strain can promote crop growth by supplying nitrogen nutrients by nitrogen-fixing.

The multiple genes related to phosphorus solubilization in the complete genome of strain TH7-28^T were identified from the genomic data. The pstS gene (phosphate substrate-binding protein) and pstA/pstB/pstC genes (ABC transporter permease subunits), constituted a functional complex involved in phosphorus acquisition and assimilation. Genes involved in the phosphorus starvation response, including phoH (encoding the phosphate starvation-inducible protein), phoR/phoP (OmpR family two-component system regulating alkaline phosphatase synthesis via sensor kinase PhoR [EC:2.7.13.3] and response regulator PhoP), and phoA (encoding alkaline phosphatase), collectively constituted a network for phosphorus acquisition. Beyond its capacity to dissolve inorganic phosphorus, the extensive collection of phospholipase-encoding genes strongly suggests that strain TH7-28^T demonstrates a potential for solubilizing organic phosphorus.

Consequently, Strain TH7-28^T employs multiple plant growth-promoting mechanisms: (1) Pathogen suppression via production of antifungal compounds; (2) Biological nitrogen fixation through expression of nitrogenase gene clusters (nifH/D/K); (3) Organic phosphorus mobilization by secreting alkaline phosphatase (phoA) and activating the phosphate starvation response regulon (phoH and phoR/phoP two-component system). Genomic annotation of strain TH7-28^T identified plant growth prompting functional genes, with comparative analysis against related Paenibacillus species revealing abundant and distinctive genetic features (Table S4).

Experimental validation results on the functional capabilities

The experimental testing results of macromolecular degradation demonstrated that strain TH7-28^T exhibits multifunctional biodegradation capabilities, including cellulose, starch, casein, and lecithin hydrolysis (Fig. 6; Table S5). The measurement results of quantitative enzyme activity, revealing nitrogenase (0.164 ± 0.006 U/mL), chitinase (8.12 ± 0.66 × 10^–3 U/mL), and β−1,3-glucanase (0.023 ± 0.004 U/mL) activities (Table S5), verified that the strain had plant growth prompting potential by nitrogen-fixing and antifungal enzymes, beyond the ability of phosphorus dissolving. The experimental validation aligned with the genomic predictions, confirming the strain's capacity for diverse biomacromolecule decomposition and plant growth promotion.

Furtherly, the plant growth-promoting activity of strain TH7-28^T was verified through the bud formation. Results showed that the germination rate of wheat seeds on the first day in the TH7-28^T bacterial solution was 94.33% ± 1.25%, which was 5.99% higher than that of the blank control, indicating that strain TH7-28^T has a good ability to promote the seed germination. The wheat growth was observed and results were shown in Fig. 7. At different days, the shoot length of seedings in the TH7-28^T treatment group was significantly better than that of the blank control group (P < 0.05), indicating that strain TH7-28^T has potential ability to promote the growth of wheat.

Fig. 7.

The results of the wheat germination under the treatment of strain TH7-28^T. a the wheat germination conditions on the first day of the control group (CK) and the TH7-28^T treatment group; b bud length of the CK group and the TH7-28^T treatment group (* indicates significant difference, *, P < 0.05; **, P < 0.01), the bar chart was plotted using Graphpad Prism version 8.0.2 (263), and the significance was analyzed using the t-test; c the growth conditions of wheat in the CK group and the TH7-28 treatment group on the 3rd, 5th, and 7th days

Description of Paenibacillus lacisediminis sp. nov.

Paenibacillus lacisediminis (la.ci.se.di′mi.nis. L. masc. n. lacus, a lake; L. neut. n. sedimen, sediment; N.L. gen. n. lacisediminis, of lake sediment).

Colonies on TSA agar are white, convex, circular, and approximately 1.2–2.5 mm in diameter. Cells are Gram-stain-positive, rod-shaped with 0.2–0.5 µm in width and 1.4–2.4 µm in length. Growth occurs at 20–55 °C (optimum, 45 °C), pH 6.0–9.0 (optimum, pH 7.5) and in the presence of 0–4.5%(w/v) NaCl (optimum, 1.5%). Cells are oxidase-and catalase-positive, but urease-negative. Nitrate reduction and indole production are positive, but negative for nitrite reduction, denitrification, and H₂S production. Hydrolysis of Tween-80 and gelatin is negative, whereas starch, cellulose, lecithin, casein, and skimmed milk are not. Glycerol, D-mannose, sucrose, D-xylose, xylan, D-raffinose, D-glucose, maltose monohydrate, ribose, D-galactose, mannitol, L-arabinose, L-rhamnose, lactose, and D-fructose are assimilated, but sorbitol, D-trehalose, ethanol, glycine, adenosine, glutamic acid, aspartate, lysine, or cysteine are not. The menaquinone is MK-7. The major fatty acids (> 10%) are anteiso-C_15:0, and summed feature 8 (comprising C_18:1 ω7c and/or C_18:1 ω6c).

The type strain is TH7-28^T (= MCCC 1K09615^T), isolated from soil sediment from Taihu Lake, PR China. The genome size of the strain is 7279 kb, with a DNA G + C content of 52.1%, as determined from its genome sequence. The GenBank accession numbers for the 16S rRNA gene and whole-genome sequences are PQ816947 and JBKIAX000000000, respectively.

Discussion

The Paenibacillus genus has attracted much attention due to its significant potential in various industrial processes and sustainable agriculture. It is widely distributed in nature and exhibits extensive environmental adaptability, which have been isolated from diverse habits such as soil, water, feed, insects, rhizosphere, and plants [23].

In this study, a bacterial strain, TH7-28^T, was isolated from the sediment of Taihu Lake, China. Based on the polyphasic taxonomic identification including phenotype, genotype and phylogenetic analysis, the isolate was disclosed to represent a novel species within the genus Paenibacillus. It had abilities to utilize various macromolecular substances, fix nitrogen and dissolve phosphorus, which may provide strong assistance for its adaptation to the environment of lake sediment. Although the description of species Paenibacillus lacisediminis sp. nov. has certain limitations based on a single isolate, in the context of ecological isolation and sampling constraints, the use of a single strain can provide valuable initial insights into the novelty and ecological role of it based on the polyphasic taxonomic identification with reference type strains.

The genomic analysis indicated that strain TH7-28^T has the function to degrade different kinds of biomacromolecules. Experiments also verified that strain TH7-28^T could degrade cellulose, starch, casein, and lecithin. Cellulose, starch, casein, and lecithin are all important biological macromolecules, and their degradation mainly depends on various hydrolases [64]. Studies have shown that Paenibacillus stains have the ability to degrade biological macromolecules, but different species can degrade different types of macromolecules, along with differing capability level [20]. The disparities in the hydrolytic capacity for biomacromolecules primarily stem from variations in both the types and quantities of genes that encode hydrolases for various substances [78]. Hence, we conducted a comparative analysis of the hydrolase genes between strain TH7-28^T and its closely related Paenibacillus strains. Our findings revealed that strain TH7-28^T exhibited a notably higher number of both gene types and gene copy numbers compared to the other reference strains. The difference in genes associated with the hydrolysis of biological macromolecules were most pronounced in the context of casein and lecithin hydrolysis. The strain TH7-28^T had genes gluP and lasA encoding rhomboid protease GluP [EC: 3.4.21.105] and LasA protease [EC: 3.4.24. -], whereas the other reference strains did not. The hydrolysis of lecithin mainly relies on various phospholipase enzymes [7]. Strains TH7-28^T contain genes encoding phospholipase A1 [EC: 3.1.1.32], phospholipase C [EC: 3.1.4.3], phospholipase D1/2 [EC: 3.1.4.4], cardiolipin-specific phospholipase [EC: 3.1.1. -] and lysophospholipase [EC: 3.1.1.5], while the other reference strains do not contain the above genes.

Nitrogen is an essential element for plant growth, but most plants cannot fix nitrogen by themselves. The intake of nitrogen mainly depends on the application of chemical fertilizers, but this is a pressure on the soil health [86]. Azobacterium can convert ineffective nitrogen into effective forms for plants to use, and some Paenibacillus strains have been reported to have nitrogen fixation ability [41], such as P. polymyxa [21], P. borealis, P. macerans, P. odorifer and P. peoriae [73]. The genome of strain TH7-28^T contains multiple nitrogen fixation genes (nifH, nifD, nifK, nifE, nifN, nifB, nifX, and iscU), which determined that it had excellent nitrogen fixation potential, thereby broadening the strain resource pool of Paenibacillus in the realm of nitrogen fixing capabilities.

The inhibition of fungal pathogens is a major challenge faced by modern agriculture. The plant growth-promoting bacteria (PGPB) could inhibit the growth of pathogenic fungi, using as an environmental friendly alternative to chemical fungicides [42]. Paenibacillus are considered to be the efficient PGPB due to their strong resistance to spores. A portion of Paenibacillus strains including P. polymyxa, P. illinoisensis KJA-424, P. lentimorbus B-30488, and P. elgii JCK1400, were reported to have the ability for anti-pathogenic fungi. The cell walls of most plant pathogenic fungi are composed of β−1,3-glucan and chitin. The hydrolysis of pathogenic fungal cell walls by β−1,3-glucanase and chitinase is the main way of PGPB inhibition of pathogenic fungi [16]. In this study, the genes encoding endo-1,3 (4 -beta-glucanase [EC: 3.2.1.6] and endo-1,3 (4 -beta-glucanase [EC: 3.2.1.6] were annotated in the genome of strain TH7-28^T. The activities of chitinase and β−1,3-glucanase were both quantitatively measured from strain TH7-28^T, which verified its capacity.

The application of Paenibacillus in agriculture mainly includes two aspects including promoting plant growth and biologically controlling of plant diseases [14]. Research reported on the plant growth-promoting properties of P. polymyxa mainly included N-fixation, P-solubilization, iron uptake and the synthesis of phytohormones [20]. Species such as P. ottowii, P. polymyxa, and P. dendritiformis all exhibited excellent antibacterial activity [13, 34]. Combined inoculation of P. polymyxa and P. lentimorbus was found to suppress the disease complex caused by root-knot nematode and wilt fungus Fusarium, which improved the plant growth under pot culture conditions [66]. In this study, genomic analysis indicates that strain TH7-28^T has the potential to degrade macromolecules, inhibit the growth of pathogenic fungi, fix nitrogen gas and dissolve phosphorus. This was confirmed by the quantitative measurement activities of cellulase, nitrogenase, chitinase and β−1,3-glucanase from the strain.

Additionally, the crop-promoting ability of strain TH7-28^T was verified through wheat germination, indicating its function as crop probiotics. However, the current plant growth-promotion assays indeed have limitations base on the fact that they are confined to just one plant species, wheat, and only assess early-stage growth parameters like seed germination rate and shoot length. It is essential to gather further supporting evidence, such as data on root development, biomass accumulation, nutrient uptake from pot culture or field trials, before extrapolating the results to broader agricultural scenarios.

As a novel species endowed with the ability to degrade biological macromolecules and foster plant growth, strain TH7-28^T holds potentials as an alternative resource of Paenibacillus species in agricultural and biotechnological applications.

Conclusion

A bacterial strain, TH7-28^T, was isolated from lake sediment and polyphasically identified as a type strain to represent a novel species Paenibacillus lacisediminis sp. nov. Genomic sequencing revealed multifunctional gene clusters encoding carbohydrate-active enzymes (cellulose and amylase), proteases, and phospholipases, alongside antifungal chitinase and endo-β-1,3-glucanase. Nitrogen-fixing potential was confirmed via nifH/D/K genes. The phosphorus transformation capacity was demonstrated through pstS/C/A/B-mediated inorganic uptake and phospholipase-driven organic solubilization. Experimental assays demonstrated significant enzymatic activities including chitinase, β-1,3-glucanase and nitrogenase, with concurrent hydrolysis of casein and lecithin. The germination rate and growth of wheat was enhanced by strain TH7-28^T. These findings establish Paenibacillus lacisediminis sp. nov. as a biotechnologically valuable resource for sustainable agriculture and macromolecules degradation, which will certainly put new light on the functional diversity of the Paenibacillus genus.

Abbreviations

AL

Amino lipid

ANI

Average nucleotide identity

CARD

Comprehensive antibiotic resistance database

CDS

Coding sequence

COG

Cluster of Orthologous Groups of proteins

dDDH

Digital DNA-DNA hybridization

GGDC

Genome-to-genome distance calculator

KEGG

Kyoto encyclopedia of genes and genomes

OGRIs

Overall genome-relatedness indices

TLC

Thin layer chromatography

TSA

Tryptic soy agar

TYGS

Type strain genome server

WGS

Whole genome sequencing

Authors’ contributions

Shuang Liu: Methodology, Investigation, Writing-Original Draft. Mei Zhai: Software, Laboratory Experiments, Writing-Revision. Jian-Hang Qu*: Conceptualization, Supervision, Writing-Review and final Approval. Lei-Zhen Zhao: Writing-Review & Editing. Jing-Xue Zhang: Software, Laboratory Experiments. Wen-Wen Ma: Software, Visualization and Graphic Design. Shuai Zhao: Investigation, Laboratory Experiments. Jia Zhou: Software, Sample Collection. Feng Huang: Data Curation, Visualization. Bo-Yuan Zhang: Statistical Analysis.

Funding

This work was supported by Key Research and Development Program of Henan Province (No. 261111114600), and International Science and Technology Cooperation Project of Henan Province (242102520024).

Data availability

The sequence of the 16S rRNA gene was submitted to the NCBI database with the accession number PQ816947. The Whole Genome Shotgun project has been also deposited in the NCBI database under the BioProject number PRJNA1204380 and the genome accession number JBKIAX000000000.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Competing interests

The authors declare no competing interests.