Microbial Ecology (2023) 86:959–972

https://doi.org/10.1007/s00248-022-02156-9

ENVIRONMENTAL MICROBIOLOGY

Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect

on Tomato Growth
Mauro Guadalupe Martínez‑Yáñez1 · Claudia Olivia Silva‑Ortega2 · Víctor Adrián Hernández‑Aranda1 ·
Moisés Roberto Vallejo‑Pérez3 · Ricardo Alcalá‑Briseño4 · Delia Xochil Vega‑Manriquez1 · Gisela Aguilar‑Benítez1 ·
Ramón Jarquin‑Gálvez1 · José Pablo Lara‑Ávila1

Received: 8 August 2022 / Accepted: 6 December 2022 / Published online: 15 December 2022
© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2022

Abstract
Mature composts and their water-based extracts, known as aerated compost teas (ACTs), are biofertilizers that share bioactive
effects like soil restoration and plant health promotion, widely used for sustainable agriculture. Bioactive effects of compost
and ACTs could be associated with their physicochemical and biological characteristics, like carbon/nitrogen (C/N) ratio
and microbiota structure respectively. In our study, we elaborated ACTs using mature homemade compost, wheat bran, and
grass clippings, following the C/N ratio criteria. Irrigation of tomato plantlets with ACT whose C/N ratio was close to the
expected C/N ratio for mature compost evidenced plant growth promotion. Exploring the bacterial microbiota of elaborated
ACTs and origin compost revealed significant structural differences, including phyla involved in N mineralization and free-
living N-fixing bacteria. Therefore, ACTs harbor diverse bacterial microbiota involved in the N cycle, which would enrich
plant and soil bacterial communities at the taxonomic and functional levels. Furthermore, ACTs are considered a part of
agroecological and circular economy approaches.

Keywords Agroecology · Biofertilizers · Microbiota · Plant growth promotion · 16S rRNA metabarcoding

Introduction The bioactive effects of the compost may be linked to

Intensive agriculture uses extensively inorganic fertilizers
that are damaging to the environment. The alternative is to
elaborate and apply stable and innocuous compost enriched
with microorganisms that reuse and reduces the accumu-
lation of waste from agriculture [1, 2]. Mature compost
promotes plant growth, controls soil-borne diseases, and
induces soil rehabilitation [3–5].
* José Pablo Lara‑Ávila
pablo.lara@uaslp.mx
1
Facultad de Agronomía y Veterinaria, Universidad
Autónoma de San Luis Potosí, Soledad de Graciano Sánchez,
SLP, México
2
San Luis Potosí, SLP, México
3
CONACYT​, Universidad Autónoma de San Luis
Potosí. Coordinación para la Innovación y Aplicación de la
Ciencia y la Tecnología (CIACYT), San Luis Potosí, SLP,
México
4
Botany and Plant Pathology, Oregon State University,
Corvallis, OR, USA
the diversity and the ability of soil colonization of micro-
organisms and their interaction with plants [5, 6]. In this
sense, compost microbiome exhibits two components: (i)
taxonomic diversity, which refers to the identity of members
of the microbial community (also known as the microbiota),
and (ii) functional diversity, which refers to the genes and
biological functions of microorganisms, for example, nitro-
gen (N) and carbon (C) cycles, and bioconversion of plant
biomass [7–9].
Regarding N and C cycles, the carbon/nitrogen (C/N)
ratio is a physicochemical parameter linked to the micro-
bial metabolic activity harbored by mature compost
[10–12]. Mineralization in a compost (occurs at C/N
ratio < 15:1) refers to the bioconversion of organic N to
inorganic N ­(NH4+, ­NO3−, ­NO2−), which is available for
plant root absorption. The lower the C/N ratios, the higher
rate of mineralization will be. Immobilization of N (C/N
ratio > 35:1) refers to bioconversion of inorganic N to
organic N. Compost whose C/N ratio is 20:1 to 301:1,
indicating an equilibrium between mineralization and

13
Vol.:(0123456789)
960 M. G. Martínez‑Yáñez et al.

immobilization. In mature compost, the C/N ratio of 10:1 Table 1  Physicochemical parameters of materials used for ACT elab-
to 15:1 can influence bioactive properties [8, 10, 13]. oration
Water-based compost extracts or aerated compost teas Parameters Grass residues Wheat bran Home-
(ACTs) are considered liquid formulations of mature com- made
post, providing soluble nutrients and microbial diversity compost
for soil enrichment and plant nutrition. Composts and pH 6.5 6.5 7.4
ACTs share bioactive effects to promote plant growth and Electrical conductivity 6.8 0.22 0.363
as biological control of plant diseases [14, 15]. Compost (S/m)
and ACTs emerge as alternatives to inorganic fertilizers Moisture (%) 21.90 23.31 21.64
and contribute positively to a circular economy and sus- Organic matter (%) 29.2 31.08 7.73
tainable agriculture [16]. Nitrogen (%) 0.89 1.03 1.05
In our study, we hypothesized that the C/N ratio of ACT Phosphorous (%) 0.17 0.42 0.35
reflects both bacterial and functional diversity and influ- Potassium (K) 0.77 0.68 2.61
ences ACT bioactivity. Then, the microbiota generated Carbon 32.68 31.19 30.69
under specific conditions would be related to ACT bioac- C/N* 36:1 30:1 29:1
tivity. As a proof of concept, we elaborated ACTs on-farm *
C/N ratio of inputs: ≤ 20:1 more convenient for N content; ≤ 27:1
conditions following criteria about the C/N ratio using moderately adequate; ≤ 208:1 less suitable[1]
mature homemade compost and plant residues (wheat
bran and grass clippings). To address ACT bioactivity,
we measure plant growth traits of ACT-irrigated tomato Effect of ACT on Seed Germination of Tomato
plantlets and explored the bacterial microbiota of elabo-
rated ACTs. We evaluated the effect of elaborated ACTs on seed ger-
mination of tomato cv. Paisano (Caloro Inc. Guadalajara,
Jalisco, Mexico). The ACTs were 1:10 diluted with sterile
distilled water and applied to peat moss as a substrate, pre-
Materials and Methods viously sterilized in an autoclave (120 °C, 15 Lb, 15 min).
The diluted ACT was applied to each substrate until moist
Elaboration of ACT​ and placed on seedbeds of 210 ml per well. Tomato seeds
were planted in the seedbeds (40 wells, 1 seed/well). The
Three ACTs were elaborated using mature homemade seedbeds were sprayed once a week with 1:10 dilutions
compost + wheat bran (ACT1), mature homemade com- of each ACT, watered as needed, and maintained under
post + grass clippings (ACT2), and homemade mature com- greenhouse conditions at 28 °C. The treatment control
post (ACT3). Thermophilic homemade compost was previ- consisted of watered peat moss substrate. Seed germina-
ously elaborated with chopped nopal (Opuntia indica) (C: tion was recorded every day for each treatment for 14 days.
5.13%; N: 0.05%), dry cattle manure (C: 53.44%; N: 1.67%), The germination experiment ended when 100% germina-
and soil from the Experimental Agroecology Unit at Facul- tion was reached in the treatment control, and there was
tad de Agronomía y Veterinaria UASLP. The moisture, C, no change in the number of germinated plants for at least
and N content of homemade compost, wheat bran, and grass 2 days.
clippings were used to calculate the required proportions of
each material in each ACT (Table 1). The three mixes whose
initial C/N ratio was elaborated between intervals of 25:1 Effect of ACTs on Plant Growth Promotion
to 35:1, calculated with software available (http://​compo​st.​
css.​corne​ll.​edu/​calc/2.​html, accessed on June 29th, 2018) Plant growth promotion was evaluated in 13 tomato plant-
from Cornel Waste Management Institute, Department of lets by triplicate for each ACT and treatment control,
Crop and Soil Sciences, Cornell University. The three ACTs tomato plantlets were obtained from the germination test.
were elaborated by mixing the inputs according to Table 2 in Each tomato plantlet group was irrigated with a 1:10 dilu-
Erlenmeyer flasks with 1 L of water. The ACTs were incu- tion of each ACT once a week, watered as needed, and
bated at 28 °C for 4 days with constant agitation at 150 rpm. maintained under greenhouse conditions at 28 °C. Tomato
Each ACT supernatant was removed and stored at 4 °C until plantlets of treatment control were water-irrigated. Twenty
application. The physicochemical parameters pH, electrical days after peak germination, we counted the number of
conductivity, moisture, organic matter, nitrogen (N), phos- leaves and measured the plantlet stem thickness and root
phorous (P), carbon (C), and C/N ratio were determined for length for each treatment with a vernier. The leaf area
each ACT (Table 2).

13
Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth 961

Table 2  Physicochemical Parameter ACT1 ACT2 ACT3 Desirable

parameters and composition of characteristics
elaborated ACTs for mature
compost**

Initial composition* 30 g WB 10 g G 50 g C Material mix

10 g C 60 g C ciC/N: 29.14:1 whose initial
ciC/N: 29.8:1 ciC/N: 30.07:1 C/N: 25:1 to
35:1
pH 6.5 7.8 7.4 6.5–8.5
Electrical conductivity (S/m) 0.298 0.322 0.341 0–0.4
Organic matter (%) 32.47 31.19 39.46 > 20
N (%) 1.233 0.595 19.728 1–3
P (%) 0.262 0.018 0.017 0.5–1
K (%) 0.323 0.383 0.518 1–1.5
C (%) 6.9 5.48 6.78 N. A
Final C/N 5.59:1 9.21:1 0.34:1 10:1 to 15:1
*
WB, wheat bran; C, mature home-made compost; G, grass residues; ciC/N, calculated initial C/N ratio
**
According to[1]

was calculated with the ImageJ software [17]. We used
the Tukey statistical test with 95% interval confidence to
differentiate among ACT treatments.
16S rRNA Gene Amplicon‑Based Metagenomic
Analysis of ACTs
Genomic DNA from ACT1, ACT2, ACT3, and the home-
made mature compost was extracted using PowerMax Soil
(MO BIO Laboratories, Carlsbad, CA, USA) in tripli-
cate, following the manufacturer’s recommendations. The
genomic DNA extraction from ACTs required a previous
centrifugation step (13,000 rpm, 10 min) to collect sus-
pended cells in ACTs. The bottom sediment of each ACTs
was used for genomic DNA extraction. The 16S rRNA gene
V4 variable region was PCR amplified using the primers
515F/806R with the barcode on the forward primer [18].
These oligonucleotides were used in a 35-cycle PCR with
HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the
following conditions: 94 °C for 3 min, followed by 35 cycles
of 94 °C for 30 s, 53 °C for 40 s, and 72 °C for 1 min,
after which a final elongation step at 72 °C for 5 min was
performed. The PCR products were run in 2% agarose gel,
and multiple samples with similar DNA concentrations were
pooled together and purified using calibrated Ampure XP
beads (Beckman Coulter Inc. Indianapolis, IN, USA). Then
the purified pooled PCR products were used to prepare Illu-
mina TruSeq DNA libraries following the manufacturer’s
recommendation (Illumina, San Diego, CA, USA). Illumina
sequencing (2 × 250 paired-end reads) was done on a MiSeq
platform (MR DNA Laboratories www.​mrdna​lab.​com/,
Shallowater, TX, USA). An average of 53,068 reads per
library were processed using the MR DNA analysis pipeline
(MR DNA Laboratories, Shallowater, TX, USA). Briefly, the
sequences were paired, the barcodes trimmed, and sequences
lower than 150 bp and ambiguous base calls were removed.
The quality reads were denoised and used to generate opera-
tional taxonomic units (OTUs) which are adequate to cap-
ture the community complexity of bacterial communities
[19]. OTUs were defined by clustering at 3% divergence
(97% similarity), and chimeric sequences were removed.
The OTUs were classified taxonomically using BLASTn
against a curated database derived from GreenGenes [20],
RDPII (www.r​ dp.c​ me.m​ su.e​ du), and NCBI (www.n​ cbi.n​ lm.​
nih.​gov). ACT 16S rRNA gene amplicon sequencing can
be retrieved from the NCBI database through BioProject
PRJNA842379.
Exploration of bacterial diversity was conducted in the
module Marker Data Profile (MDP) in MicrobiomeAnalyst
(accessed on October 11th, 2021) [21, 22]. Data were filtered
for low count (4 counts and 20% prevalence in samples)
and variance (10% to remove based on interquartile range).
Data normalization was performed through total sum scaling
(TSS) and rarefying to the minimum library size (20 steps).
Average Good’s coverage was calculated for each sample
in the rarefaction plot. Species richness (number of taxa in
a community), Shannon, and Chao1 diversity indices were
calculated to obtain the α-diversity at the genus level. The
differences in α-diversity among groups were statistically
evaluated using the Kruskal–Wallis test. The β-diversity
at the genus level was calculated using the Bray–Curtis
dissimilarity index and visualized through principal coor-
dinate analysis (PCoA). The statistical differences among
β-diversity indices were evaluated using permutational mul-
tivariate analysis of variance (PERMANOVA). Difference
comparison between the microbial composition of ACTs and

13
962 M. G. Martínez‑Yáñez et al.

compost samples was calculated through linear discriminant

analysis (LDA) effect size (LEfSe) with a p-value cutoff of
0.01 and Log LDA score > 2, at the genus level. Correla-
tion network analysis at the phylum level was performed
using the SparCC correlation algorithm, 100 permutations,
p-value 0.05, and correlation threshold 0.3. Core bacte-
rial microbiota at the phylum and genus level was defined
using a threshold of 0.01% relative abundance. Hierarchical
clustering and heatmap visualization were performed at the
phylum and genus level, by using the Euclidean distance
measure and average linkage clustering method [23].
Fig. 1  Effect of ACTs on germination of tomato seeds

Results
ACT Elaboration
The physicochemical characteristics of homemade mature
compost, grass clippings, and wheat bran are shown in
Table 1. These materials should be considered moder-
ately adequate for composting based on the C/N ratio,
respectively.
The composition and the calculated initial C/N ratio for
each ACT mixture, also the physicochemical characteristics
of the elaborated three ACTs are shown in Table 2. The final
C/N ratio showed differences between ACTs. Specifically,
ACT2 showed the C/N ratio (9.2:1) closer to the expected
interval for a mature compost (< 10:1). Other physico-
chemical characteristics such as pH, electrical conductiv-
ity, organic matter, N, P, K, and C content were within the
expected interval for mature compost in each ACT.
Plant Growth–Promoting Traits of ACTs
Seeds treated with ACT1, ACT2 and ACT3 showed 48%,
89%, and 53% germination rates 7 days after sowing (das).
The treatment control group showed a 79% germination rate
at 7 das. The seeds treated with ACT2, and the treatment
control showed 100% germination at 9 and 13 days, respec-
tively. Treatments with ACT1 and ACT3 showed 92% and
89% germination rates at 14 days, respectively (Fig. 1).
The tomato plantlets obtained from the previous germi-
nation test were transplanted and irrigated with 1:10 dilu-
tion ACT or water (treatment control) to evaluate the plant
growth promotion of each ACT. The stem thickness, number
of leaves, leaf area, and root length were measured 21 days
after transplanting (dat). The stem thickness of tomato plant-
lets treated with ACT1, ACT2, and ACT3 showed an aver-
age diameter of 0.142 cm, 0.206 cm, and 0.14 cm, respec-
tively. The treatment control showed an average of 0.177 cm
in diameter. A comparison of the means using the Tukey test
showed that ACT2 was statistically different from ACT1,
ACT3, and the treatment control. ACT1 and ACT3 showed
no statistical differences among them (Fig. 2a).
Regarding the number of leaves, ACT2 showed the high-
est number of leaves, followed by plantlets of the treatment
control. The Tukey test showed that ACT2 was statistically
different from ACT1 and ACT3, and the treatment con-
trol. No significant differences were found between ACT1
and ACT3 treatments (Fig. 2b). The largest leaf area was
observed for plantlets treated with ACT2. The Tukey test
showed that ACT2 statistically differed from ACT1 and
ACT3 treatments and the treatment control (Fig. 2c). The
root length had no significant differences in any treatments,
ACT1, ACT2, ACT3, and the treatment control.
Bacterial Diversity of Bioactive ACTs
To evaluate the microbial foundations of ACTs, we explored
the bacterial microbiota of elaborated ACTs and homemade
mature compost (hereafter compost), through 16S rRNA-
based metagenomic survey. A total of 522,188 sequences
were obtained, with average sequences per sample of 43,515,
maximum sequences per sample 54,427, and minimum
counts per sample 33,102. A total of 495 OTUs of which
488 OTUs with ≥ 2 counts. The filtering step in Microbi-
omeAnalyst yielded a total of 160 low-abundance OTUs that
were removed based on prevalence. A total of 33 low-vari-
ance OTUs were removed based on the interquartile range.
The number of OTUs after the data filtering step was 295
(Table S1).
The α-diversity was calculated using the Richness
(observed taxa), Shannon, and Chao1 diversity indices for
each ACT and compost sample. ACT1, ACT3, and compost
had higher α-diversity than ACT2. The α-diversity of ACT3
was higher than ACT2 but lower than ACT1 and compost
(Fig. 3a, b, c). ACTs and compost samples were rarefied
to a minimum library size 33,068 sequences to calculate
α-diversity parameters. Rarefaction is a tool to normalize
library sizes for diversity analyses. The method is a random
subsampling without replacement, to the size of the smallest

13
Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth 963
Fig. 2  Plant growth promotion traits of ACTs on tomato plantlets. Stem thickness (a), number of leaves (b), leaf area (c). The differences among
treatments were determined using the Tukey test at 95% interval confidence. Different letters show significant differences
size library. Then plotting the number of species was calcu-
lated at iteration on each sample [24]. The rarefaction plot
showed a similar pattern to α-diversity, suggesting species
richness is higher in ACT1, ACT3, and compost than in
ACT2 samples (Fig. 3d). It is noteworthy that ACTs and
compost samples reached a plateau in the rarefaction plot,
also average Good’s coverage (refers to the percent of the
total species represented in a sample) suggested that esti-
mated 99.93% of the total species is represented in respec-
tive samples. It means that biodiversity was suitably sam-
pled; therefore, α-diversity was properly rated. In general
terms, the evidence may suggest more different bacteria
species in ACT1, ACT3, and compost than in ACT2.
The β-diversity revealed statistical differences between
the bacterial microbiota of ACT1 and compost compared
to ACT2 and ACT3 samples (F-value: 103.9, R2 0.97498,
p-value < 0.001). The comparison between ACT2 and ACT3
samples was statistically significant (p-value < 0.001); how-
ever, there were no statistical differences between ACT1 and
compost samples. The β-diversity was visualized using a
PCoA, explaining 61% and 29% of the observed variation
on axes 1 and 2, respectively. Consequently, the bacterial
microbiota of ACT2 differed from ACT3, ACT1, and com-
post. The bacterial microbiota of ACT1 and compost showed
similarities (Fig. 3e).
Based on genera relative abundance, the bacterial taxo-
nomic composition was heterogeneous among ACTs and
compost samples. The top 25 most abundant genera are
shown in Fig. 4. The most abundant genera for ACT1 were
Acidovorax (Proteobacteria), Lewinella (Bacteroidetes),
Sneathiella (Proteobacteria) and Thalassospira (Proteo-
bacteria). Regarding ACT2 were Weissella (Firmicutes),
Clostridium (Firmicutes), Pediococcus (Firmicutes), Azo-
tobacter (Proteobacteria), and Pantoea (Proteobacteria).
In relation to ACT3 were Pseudomonas (Proteobacteria),
Paenibacillus (Firmicutes), and Pantoea (Proteobacteria).
In the compost sample, the most abundant genera were
Acidovorax (Proteobacteria), Sphingobacterium (Bacteroi-
detes), Sinorhizobium (Proteobacteria), Sneathiella (Pro-
teobacteria), Lewinella (Bacteroidetes), and Cytophaga
(Bacteroidetes).
To identify genera with significantly different abundances
between ACTs and compost, interpreted as biomarker genera
for each sample, we applied the LEfSe approach (Fig. 5).
Lewinella (Bacteroidetes), Acidovorax (Proteobacteria),
Thalassospira (Proteobacteria) and Gracilimonas (Balne-
olaeota) showed significantly higher abundance and could
be considered as biomarkers of ACT1. Regarding ACT2,
Weissella (Firmicutes), Clostridium (Firmicutes), Azotobac-
ter (Proteobacteria) and Lactobacillus (Firmicutes) could be
considered biomarkers. In ACT3, the biomarker genera were
Pseudomonas (Proteobacteria), Pantoea (Proteobacteria),
Cellvibrio (Proteobacteria), Paenibacillus (Firmicutes),
Xanthomonas (Proteobacteria) and Pseudoxanthomonas
(Proteobacteria). In relation to the compost, the biomarker
genera were Pediococcus (Firmicutes), Sneathiella (Proteo-
bacteria), Parapedobacter (Bacteroidetes), Opitutus (Ver-
rucomicrobia), and Sinorhizobium (Proteobacteria). The
biomarker genera in each ACT differed from compost and
among ACTs.
Potential interactions between phyla were revealed
through SparCC network analysis. A total of 50 interac-
tions were identified among 14 phyla, whose showed dif-
ferences in relative abundances between the ACTs and
compost samples. In total, 32 positive interactions and 18
negative interactions were identified (Fig. 6a). Interestingly,
the phylum Firmicutes was detected in higher abundance in
ACT2 (Fig. 6b), showing a unique negative interaction with
13
964
Fig. 3  Alpha and beta diversity of bacterial microbiota of ACTs
and compost. Richness: p-value 0.022446, Kruskal–Wallis statistic
9.5848 (a). Shannon index: p-value 0.015564, Kruskal–Wallis sta-
tistic 10.385 (b). Chao1 index: p-value 0.021623, Kruskal–Wallis
statistic 9.6667 (c). Rarefaction curves. Average Good’s coverage:
the Deinococcus-Thermus group. It is noteworthy that the
Deinococcus-Thermus group was detected at higher levels
in ACT1, ACT3, and compost samples showing 12 interac-
tions (Fig. 6c). Deinococcus-Thermus group showed posi-
tive interactions with Chlorobi, Gemmatimonadetes, Planc-
tomycetes, Chloroflexi, Verrucomicrobia, Bacteroidetes, and
Armatinonadetes, which also had negative interactions with
Acidobacteria, Firmicutes, Cyanobacteria, Spirochaetes,
and Thaumarcheota.
The core bacterial microbiota refers to the set of taxa
that were detected in a high fraction of a population above
a given relative abundance as a threshold, which was com-
posed of Proteobacteria, Bacteroidetes, Firmicutes, Act-
inobacteria, Verrucomicrobia, Planctomyces, Chloroflexi,
Deinococcus-Thermus group, and Fibrobacteres. In this
13
M. G. Martínez‑Yáñez et al.
99.96% ± 0.01 for ACT1, 99.87% ± 0.02 for ACT2, 99.95% ± 0.01 for
ACT3, 99.95% ± 0.001 for compost (d). Principal coordinate analysis
(PCoA) based on pairwise Bray–Curtis dissimilarity, PERMANOVA
F-value: 103.9, R.2 0.97498, p-value < 0.001 (e)
regard, Proteobacteria and Firmicutes showed the higher
prevalence, and Fibrobacteres showed the lesser prevalence
(Fig. 7). The core bacterial microbiota at the genus level
included Parapedobacter, Pedobacter Devosia, and Sphin-
gobacterium (Bacteroidetes), Acidovorax, Sneathiella and
Sinorrhizobium (Proteobacteria), and Bacillus (Firmicutes)
at higher prevalence. Notably, Xanthomonas and Pantoea
genera were included with a lower prevalence (Fig. S1).
Hierarchical clustering heatmap visualization of ACTs
and compost bacterial microbiota at the phylum level high-
lighted the formation of 5 clusters that included phyla at
higher abundance: cluster 3 (C3) contained shared phyla
between ACT1 and compost samples, included Gemmati-
nonadetes, Chloroflexi, Deinococcus-Thermus, and Bacte-
roidetes. Clusters 1, 2, 4, and 5 contained phyla from ACT2
Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth 965

Fig. 4  Bacterial taxonomic structure of ACTs and compost based on relative abundance. The graphs showed the top 25 most abundant genera

(included Firmicutes), compost (included Cyanobacteria,
Chlorobi, Armatimonadetes, Planctomycetes, Thaumar-
chaeota), ACT1 (included Actinobacteria, Acidobacteria,
Spirochaetes), and ACT3 (included Tenericutes, Fibrobacte-
res, Proteobacteria, Verrucomicrobia), respectively (Fig. 8).
Heatmap at genus level revealed 9 clusters that comprised
genera with higher abundance in either ACTs or compost
samples. Clusters 2 and 9 included shared genera between
ACT3 and compost. Clusters 5 and 7 included shared genera
between ACT1 and compost. Clusters 4 and 6 included gen-
era from ACT1. Clusters 1, 3, and 8 included genera from
ACT2, ACT3, and compost respectively. It is noteworthy
that C5 was a cluster that included the major number of
genera. C1, C3, and C8 were smaller clusters (Fig. S2).
Phytopathogenic genera Xanthomonas, Pantoea, Xyllela,
and Agrobacterium showed higher abundance in ACT3
(Cluster 3). Whereas, the Ralstonia genus was shared
by compost and ACT1 (cluster 7) in higher abundance
(Fig. S2). It is noteworthy that no symptoms of the bacterial
disease were observed in ACT irrigated-tomato plantlets.
In summary, ACT2 was made of mature homemade
compost + grass clippings and showed a pH and C/N ratio
within the expected interval for mature compost. Also,
ACT2 promoted the plant growth of tomato plantlets. On
the other hand, the bacterial microbiota of ACTs and com-
post exhibit significant differences from each other. Some
genera were identified as specific biomarkers for each ACT
and compost of origin. Also, despite differences in bacterial

13
966
Fig. 5  Biomarkers genera in
bacterial microbiota of ACTs
and compost, based on LEfSe
approach (Top 20). Miniheat
map indicates significant abun-
dance of genera: higher (red),
and lower (blue) in each sample.
p-value cutoff 0.01, Log LDA
score > 2
structure, some phyla and genera were found as a part of
the core bacterial microbiota of ACTs and compost due to
constant association with such microhabitats. Furthermore,
data suggested potential interactions at the phylum level,
which could shape bacterial microbiota structure for each
ACT and therefore linked to the functionality of each ACT.
Discussion
Composts and ACTs are biofertilizers whose diverse micro-
biota may be linked to bioactivity, as a control disease, plant
growth promotion, and soil restoration. Microbiota and its
intrinsic metabolic activity, harbored by compost and ACTs
could lead to a biological product with capacities for N
mineralization (C/N ratio < 15:1) or N immobilization (C/N
ratio > 35:1). However, mature compost that positively influ-
ences plant growth could exhibit C/N ratio 10:1 to 15:1 [1,
25].
13
M. G. Martínez‑Yáñez et al.
ACT Microbiota Diversity
In our study, for the elaboration of ACTs as a proof of con-
cept, we employed mature homemade compost (as primary
inoculum of microbial biodiversity), grass clippings, and
wheat bran, both as additional sources of carbon and micro-
organisms. The 3 materials were considered moderately
optimal materials for the ACT elaboration, based on their
respective C/N ratio close to 27:1 [1, 10].
We elaborated 2 ACTs (ACT1: mature homemade
compost + wheat bran; ACT2: mature homemade com-
post + grass residues), a third ACT was elaborated uniquely
by using mature homemade compost (ACT3), which should
be considered a liquid formulation of mature homemade
compost. Notably, the C/N ratio of ACT2 (9.21:1) was closer
to the optimum value expected for a mature compost, so
the N mineralization rate in ACT2 should be lesser than
in ACT1 (C/N ratio 5.59:1) and ACT3 (C/N ratio 0.34:1)
[10, 13].
Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth 967

Fig. 6  Correlation network analyses at phyla level within bacte- (red) or negative (blue) correlation (a). Box plot of Firmicutes (b)
rial microbiota of ACTs and compost. Nodes represent phyla, edges and Deinococcus-Thermus group (c) showing a respective significant
represent correlation > 0.3 between pairs of phyla. The node colors abundance in ACTs and compost
indicate abundance in each sample. The edge color indicates positive

Fig. 7  Core bacterial microbiota of ACT1, ACT2, ACT3, and com- a threshold. Proteobacteria and Firmicutes showed the highest preva-
post at the phylum level. It refers to the set of taxa that were detected lence, followed by Bacteroidetes, Actinobacteria, and Verrucomicro-
in a high fraction of a population above a given relative abundance as bia. Fibrobacteres exhibited low prevalence

13
968
Fig. 8  Hierarchical clustering of the bacterial microbiota of ACTs
and compost, at the phylum level. Numbers and color nodes high-
lighted clusters with phyla that showed higher abundance in the spe-
cific ACT. It is noticeable that Firmicutes constituted cluster 1 with
a single phylum, due to the highest abundance in ACT2. Whereas
based on the higher abundance in ACT3 Verrucomicrobia, Pro-
teobacteria and Fibrobacteres were clustered in cluster 5. Cluster 2
The observed decrement in the C/N ratio in finished
ACTs may be linked to carbon bioconversion to ­CO2, assum-
ing minimal N losses as a result of microbial metabolism
[10]. The addition of wheat bran and grass clippings to
mature homemade compost for ACT1 and ACT2 elaboration
respectively should provide additional sources of microbial
diversity and C to the developing microbiota. In this regard,
the C sources incorporated from grass clippings and wheat
bran included highly and less recalcitrant compounds, like
lignin and oligosaccharides respectively, which are firstly
metabolized by microbiota [26–28]. Concerning microbial
diversity, it is noteworthy to mention that Firmicutes is a
common epiphytic phylum of switchgrass (Panicum virga-
tum L.) that should explain the higher abundance of Fir-
micutes in ACT2 microbiota [29]. So, the exploration of
13
M. G. Martínez‑Yáñez et al.
(which belonged to compost samples) was integrated by Cyanobac-
teria, Chlorobi, Amatimonadetes, Plantomycetes, and Thaumarcheota
(an archeal taxon). Cluster 3 comprised Gemmatimonadetes, Chloro-
flexi, Deinococcus-Thermus, and Bacteroidetes that were shared by
ACT1 and compost samples. Cluster 4 included Actinobacteria, Aci-
dobacteria, and Spirochaetes uniquely at ACT1, Deinococcus-Ther-
mus, and Bacteroidetes
the bacterial microbiota of ACTs and compost through 16S
metabarcoding confirmed that both C sources heterogeneity
and microbial diversity associated with the used materials
differentially affected the bacterial microbiota of each ACT
[7, 26, 30].
The evidence suggested that the ACT2 microbiota
showed lesser biodiversity than ACT1, ACT3, and compost
microbiota. It is worth mentioning that similarities were
found between the microbiota of ACT1 and homemade
mature compost, despite ACT3 being elaborated uniquely
using homemade compost. Remarkably, the microbiota of
each ACT and compost showed significant differences in the
relative abundance of determined genera in each ACT that
allowed the identification of potential biomarkers of each
ACT.
Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth 969
On this subject, a diversity of microorganisms and bacte-
rial genes involved in the N cycle was identified in our study.
Proteobacteria, Bacteroidetes, Acidobacteria, Firmicutes,
Actinobateria, and Chloroflexi were identified as a part of
the core bacterial microbiota of ACTs and compost and
showed significantly different relative abundances in each
ACT. The mentioned phyla are known to play a role in N
mineralization (C/N < 10:1) either due to ureolytic activity
(ureC), chitinolytic activity (chiA), arginase activity (rocF),
or protease activity (npr) [31]. It is worth noting that Azo-
tobacter (Proteobacteria) and Clostridium (Firmicutes)
were identified as biomarkers of the bacterial microbiota of
ACT2. Clostridium and Azotobacter are free-living bacte-
ria that perform biological nitrogen fixation (BNF), which
refers to the bioconversion of atmospheric nitrogen (­ N2) into
ammonium ­(NH3), a major source of inorganic N for plants
[32, 33].
The mentioned phyla and genera would be related to the
observed C/N ratio (< 10:1) in finished ACTs. However
higher rates of N mineralization in ACT1 and ACT3 than
in ACT2 were suggested based on respective C/N ratios.
Notably, BNF should be an active pathway in addition to
N mineralization operating in ACT2. Therefore, both taxo-
nomic and functional diversity should be related to C/N ratio
differences between ACTs [34–36].
ACT Functional Diversity Is Related to Plant Growth
Promotion Trait
It is not surprising that potential interactions at the bacte-
rial level during the ACT elaboration process allowed the
generation of a biological product with characteristic micro-
biota and ecological functions, like the N cycle and plant
disease suppression [37]. Negative interactions should occur
and shape the microbiota of respective ACT; as an exam-
ple, in our study, evidence suggested a negative correlation
between Deinococcus-Thermus and Firmicutes. Experimen-
tal evidence showed interference of biofilm formation of
Staphylococcus aureus (Firmicutes) by exopolysaccharide
of Deionococcus radiodurans [38]. The evidenced behavio-
ral regulation of Staphylococcus aureus by D. radiodurans
allowed us to speculate that a higher relative abundance of
Deinococcus-Thermus and low relative abundance of Firmi-
cutes (observed in ACT1, ACT3, and compost microbiota)
has a similar explanation. An opposite trend was observed
in ACT2 microbiota.
Notably, microbial richness and bacterial interactions
inside each ACT likely contributed to inhibiting the expres-
sion of pathogenic behavior of Ralstonia, Pantoea, Xyllela,
Xanthomonas, and Agrobacterium that showed at differential
prevalence in ACTs microbiota, which is related to plant
disease suppression trait [30].
ACT2-irrigated tomato plantlets evidenced plant growth
promotion. However, both ACT1 and ACT3-irrigated
plantlets showed less growth than ACT2-irrigated plant-
lets and treatment control. This evidence could suggest
that ACT1 and ACT3-irrigated plantlets would exhibit a
slight nutritional deficiency, taking into account that used
seeds were certified with a 90% germination rate and no
symptoms of phytotoxicity were detected. However, the
bioactive effects of compost and ACT on crops could be
variable or may not be visible in specific development
stages [39–42]. In our study, it is likely that the bioactive
effects of ACT 1 and ACT3 could be evidenced in other
phenological stages of tomato plants.
Based on the C/N ratio values of ACTs, a higher rate of
N mineralization would be expected in ACT1 and ACT3-
irrigated plantlets than in ACT2-irrigated plantlets [1, 10].
In this sense, N (­ NO3−) is a plant macronutrient required
for optimum growth and development, exhibiting high
solubility and low retention in soil. Excessive application
of ­NO3− or higher humidity levels could lead to N defi-
ciency [43–45]. The low C/N ratios observed in ACT1 and
ACT3 implied a higher rate of N ­(NO3−) releasing and los-
ing through leaching in the substrates of irrigated tomato
plantlets [46]. Consequently, ACT1 and ACT3-irrigated
plantlets should exhibit lower plant growth, as a result of
slight presumed N deficiency plantlets. In addition, to the
likely variable bioactive effect of ACT1 and ACT3.
The bacterial phyla Proteobacteria, Chloroflexi, Firmi-
cutes, and Actinobateria involved in N mineralization, also
genera Azotobacter and Clostridium, free-living N-fixers
bacteria, were identified as a part of the core bacterial
microbiota of ACT1, ACT2, ACT3, and homemade com-
post, with differences at relative abundance respectively
[47].
In this regard, ACT2 could act as a source of phyla
involved in N mineralization, and free-living N-fixer
bacteria for tomato plantlets rhizosphere. Notably, Azo-
tobacter spp. and Clostridium spp. represent a source of
­NH3, a major source of inorganic N for plants [32, 33].
Clostridium spp. is a free-living N fixer under anaerobic
conditions found in gramineous plants [48, 49]. Azotobac-
ter spp. has been associated with the enhancement of plant
nutrition and plant growth promotion traits, in sustainable
agricultural production strategies [32, 50].
In our study, despite N mineralization would occur at
substrates of ACT2-irrigated tomato plantlets, N fixation
and other mechanisms involved in plant growth promotion
would also be carried out by Azotobacter and Clostrid-
ium. The above may explain the plant growth observed in
ACT2-irrigated plantlets.
13
970
Microbiota Diversity Associated to Bioactive ACTs
and Compost
Plant growth promotion and disease suppression are bio-
active effects related to the microbiota of mature compost
and ACTs [14, 30, 42, 51, 52]. In this regard, phyla like
Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria,
Chloroflexi, Gemmatimonadetes, and Acidobacteria are
reliably found as dominant phyla in mature plant disease-
suppressive compost [26, 53]. Likewise, Bacillus (Firmi-
cutes), Ochrobactrum (Proteobacteria), and Sphingomonas
(Proteobacteria) are related to plant growth promotion of
lettuce, soybean, and sugar corn [41].
The plant growth promotion trait attributed to bacterial
phyla requires several mechanisms, among them the N cycle,
phosphate solubilization, and secondary metabolite biosyn-
thesis [52, 54–56]. Although in our study, we analyzed plant
growth of ACT-irrigated tomato plantlets, our results were
consistent with the aforementioned, since bacterial micro-
biota of ACTs and compost included phyla Proteobacteria,
Bacteroidetes, Firmicutes, and Actinobacteria with signifi-
cant differences at relative abundance. Since those phyla are
involved in the N cycle, it highlights that the C/N ratio of
ACTs could be a physicochemical indicator of their intrinsic
bacterial metabolism [52].
The microbiota complexity of compost and ACTs sug-
gests that interaction between inner microbial communities
can influence indirectly bioactive effect in planta [42, 57].
In our study, only ACT2 induced plant growth on tomato
plantlets; also, phyla Firmicutes and genus Azotobacter spp.
were detected at significantly higher relative abundance
which could be related to observed plant growth promotion.
It is likely that the bioactive effects of ACT1 and ACT3
on tomato plants would be evidenced in other physiological
and development stage since bacterial phyla involved in the
N cycle and other plant growth promotion activities were
detected as a part of core microbiota.
In summary, ACT2-irrigated tomato plantlets exhibit
plant growth promotion. It is noteworthy that ACT2 exhib-
ited a C/N ratio closer to the C/N ratio of mature composts.
Bacterial microbiota included phyla involved in N min-
eralization (Proteobacteria, Acidobacteria, Chloroflexi,
Firmicutes, Actinobateria) as a part of the core bacterial
microbiota of ACTs and homemade compost, which is
consistent with previous studies. Notably, ACT2 bacterial
microbiota included Azotobacter ssp. and Clostridium ssp.
genera involved in N fixation, as specific biomarkers. Evi-
dence could suggest that N mineralization is a permanent
trait associated with ACTs and homemade compost. We pro-
posed that differences in relative abundances of phyla and
genera involved in N mineralization and N fixation in each
ACT could yield C/N ratio differences among ACTs. Varia-
tion in the C/N ratio should be related to bacterial microbiota
13
M. G. Martínez‑Yáñez et al.
structure since the C/N ratio reflects the bacterial metabolic
diversity. Therefore, our results agree with the hypothesis
about the connection among the ACT elaboration process,
ACT microbiota diversity, C/N ratio, and plant fitness [40,
58].
Conclusion
Our results contribute to the understanding that ACTs,
homemade biofertilizers, harbor microbiota involved in
the N cycle, as a basis of plant growth promotion trait. The
respective microbiota and its intrinsic functional diversity
showed significant differences with the compost of origin,
which could be related to physicochemical properties, such
as the C/N ratio. Compost and derivatives ACTs are able
to enrich the soil and plant microbiomes at taxonomic and
functional levels, which favor soil restoration and plant
health. Production and application of compost and ACTs
provide social, economic, and ecological benefits. There-
fore, compost and ACTs are key elements for sustainable
agriculture within a circular economy framework. A gradual
decrease of agrochemicals and their substitution by biofer-
tilizers could favor the decrease of both environmental and
human health risks, also the enrichment of plant and soil
microbiomes.
Supplementary Information The online version contains supplemen-
tary material available at https://d​ oi.o​ rg/1​ 0.1​ 007/s​ 00248-0​ 22-0​ 2156-9.
Acknowledgements To Martin Escoto-Rodríguez (UASLP) who man-
aged the rehabilitation of lab spaces in Facultad de Agronomía y Vet-
erinaria UASLP. We thank the anonymous reviewers for their valuable
comments on our manuscript.
Author Contribution JPLA conceived and designed the study. COSO
and MGMY conducted experiments. MGMY, COSO, DXVM, GAB,
RJG, MRVP, and JPLA analyzed and interpreted data. VAHA and RAB
contributed analytical tools. MGMY, VAHA, RAB, and JPLA wrote
the paper. All authors read and approved the manuscript.
Funding This work was funded by the Consejo Nacional de Ciencia y
Tecnología-Secretaría de Educación Pública (CONACyT-SEP Project
236066). VAHA received a fellowship (#806623) from CONACYT for
PhD studies (CVU 1034365).
Data Availability The datasets presented in this study can be found in
online repositories. Aerated compost teas 16S rRNA-based-metagen-
omes data can be retrieved from the NCBI database through BioProject
PRJNA842379.
Declarations
Ethics Approval Not applicable.
Consent to Participate Not applicable.
Consent for Publication Not applicable.
Analysis of Bacterial Microbiota of Aerated Compost Teas and Effect on Tomato Growth 971
Conflict of Interest The authors declare no competing interests.
References
1. Ahmad R, Jilani G, Arshad M et al (2007) Bio-conversion of
organic wastes for their recycling in agriculture: an overview of
perspectives and prospects. Ann Microbiol 57:471–479
2. Rath PP, Das K, Pattanaik S (2022) Microbial activity during com-
posting and plant growth impact: a review. J Pure Appl Microbiol
16:63–73
3. Antoniou A, Tsolakidou MD, Stringlis IA, Pantelides IS (2017)
Rhizosphere microbiome recruited from a suppressive compost
improves plant fitness and increases protection against vascular
wilt pathogens of tomato. Front Plant Sci 8:2022
4. Mehta CM, Palni U, Franke-Whittle IH, Sharma AK (2014) Com-
post: its role, mechanism and impact on reducing soil-borne plant
diseases. Waste Manag 34:607–622
5. Zhen Z, Liu H, Wang N et al (2014) Effects of manure com-
post application on soil microbial community diversity and soil
microenvironments in a temperate cropland in China. PLoS ONE
9:e108555. https://​doi.​org/​10.​1371/​journ​al.​pone.​01085​55
6. Carvalhais LC, Dennis PG, Fan B et al (2013) Linking plant nutri-
tional status to plant-microbe interactions. PLoS ONE 8:e68555
7. Antunes LP, Martins LF, Pereira RV et al (2016) Microbial
community structure and dynamics in thermophilic composting
viewed through metagenomics and metatranscriptomics. Sci Rep
6:38915
8. Lazicki P, Geisseler D, Lloyd M (2020) Nitrogen mineralization
from organic amendments is variable but predictable. J Environ
Qual 49:483–495. https://​doi.​org/​10.​1002/​jeq2.​20030
9. Meng Q, Yang W, Men M et al (2019) Microbial community
succession and response to environmental variables during cow
manure and corn straw composting. Front Microbiol 10:529
10. Azim K, Soudi B, Boukhari S et al (2018) Composting param-
eters and compost quality: a literature review. Org Agr 8:141–158.
https://​doi.​org/​10.​1007/​s13165-​017-​0180-z
11. Eiland F, Klamer M, Lind AM, Leth M, Bååth E (2001) Influence
of initial C/N ratio on chemical and microbial composition during
long term composting of straw. Microb Ecol 41:272–280. https://​
doi.​org/​10.​1007/​s0024​80000​071
12. Sokač T, Valinger D, Benković M et al (2022) Application of
optimization and modeling for the composting process enhance-
ment. Processes 10:229. https://​doi.​org/​10.​3390/​pr100​20229
13. Norton JM, Schimel JP (2011) Nitrogen mineralization immobili-
zation turnover. In P. M. Huang (ed.), Handbook of Soil Science,
Second Edition ed. CRC Press.
14. González-Hernández AI, Suárez-Fernández MB, Pérez-Sánchez
R et al (2021) Compost tea induces growth and resistance against
Rhizoctonia solani and Phytophthora capsici in pepper. Agron-
omy 11:781
15. Otero M, Salcedo I, Txarterina K, González-Murua C, Duñabei-
tia MK (2020) Compost tea reduces the susceptibility of Pinus
radiata to Fusarium circinatum in nursery production. Phytopa-
thology 110:813–821
16. Sulewski P, Kais K, Gołaś M et al (2021) Home bio-waste com-
posting for the circular economy. Energies 14:6164. https://​doi.​
org/​10.​3390/​en141​96164
17. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH Image to
ImageJ: 25 years of image analysis". Nat Methods 9:671–675
18. Caporaso JG, Lauber CL, Walters WA et al (2011) Global patterns
of 16S rRNA diversity at a depth of millions of sequences per
sample. Proc Natl Acad Sci USA 108(Suppl):4516–22
19. Joos L, Beirinckx S, Haegeman A et al (2020) Daring to be differ-
ential: metabarcoding analysis of soil and plant-related microbial
communities using amplicon sequence variants and operational
taxonomical units. BMC Genomics 21:733
20. DeSantis TZ, Hugenholtz P, Larsen N et al (2006) Greengenes, a
chimera-checked 16S rRNA gene database and workbench com-
patible with ARB. Appl Environ Microbiol 72:5069–5072
21. Chong J, Liu P, Zhou G et al (2020) Using microbiomeanalyst
for comprehensive statistical, functional, and meta-analysis of
microbiome data. Nat Protoc 15:799–821. https://d​ oi.o​ rg/1​ 0.1​ 038/​
s41596-​019-​0264-1
22. Dhariwal A, Chong J, Habib S et al (2017) MicrobiomeAnalyst
- a web-based tool for comprehensive statistical, visual and meta-
analysis of microbiome data. Nucleic Acids Res 45:W180-188
23. Liu YX, Qin Y, Chen T et al (2021) A practical guide to ampli-
con and metagenomic analysis of microbiome data. Protein Cell
12:315–330
24. Cameron ES, Schmidt PJ, Tremblay BJ et al (2021) Enhancing
diversity analysis by repeatedly rarefying next generation sequenc-
ing data describing microbial communities. Sci Rep 11:22302
25. Tiquia SM (2005) Microbiological parameters as indicators of
compost maturity. J Appl Microbiol 99:816–828
26. Blaya J, Marhuenda FC, Pascual JA, Ros M (2016) Microbiota
characterization of compost using omics approaches opens
new perspectives for Phytophthora root rot control. PLoS ONE
11:e0158048
27. Danial WH, Taib RM, Samah MAA et al (2020) The valorization
of municipal grass waste for the extraction of cellulose nanocrys-
tals. RSC Adv 10:42400–42407
28. Merali Z, Collins SRA, Elliston A et al (2015) Characterization
of cell wall components of wheat bran following hydrothermal
pretreatment and fractionation. Biotechnol Biofuels 8:23
29. Hestrin R, Lee MR, Whitaker BK, Pett-Ridge J (2021) The switch-
grass microbiome: a review of structure, function, and taxonomic
distribution. Phytobiomes J 5:14–28
30. Marín F, Santos M, Diánez F et al (2013) Characters of compost
teas from different sources and their suppressive effect on fungal
phytopathogens. World J Microbiol Biotechnol 29:1371–1382
31. Ouyang Y, Norton JM (2020) Short-term nitrogen fertilization
affects microbial community composition and nitrogen minerali-
zation functions in an agricultural soil. Appl Environ Microbiol
86:e02278-e2319
32. Aasfar A, Bargaz A, Yaakoubi K et al (2021) Nitrogen fixing
Azotobacter species as potential soil biological enhancers for crop
nutrition and yield stability. Front Microbiol 12:628379
33. Santi C, Bogusz D, Franche C (2013) Biological nitrogen fixation
in non-legume plants. Ann Bot 111:743–767
34. Palese AM, Pane C, Villecco D et al (2021) Effects of organic
additives on chemical, microbiological and plant pathogen sup-
pressive properties of aerated municipal waste compost teas. Appl
Sci 11:7402. https://​doi.​org/​10.​3390/​app11​167402
35. Wang N, Li H, Wang B et al (2021) Taxonomic and functional
diversity of rhizosphere microbiome recruited from compost
synergistically determined by plant species and compost. Front
Microbiol 12:798476
36. Wang X, Reilly K, Heathcott R et al (2022) Soil nitrogen treatment
alters microbiome networks across farm niches. Front Microbiol
12:786156
37. Cuartero J, Özbolat O, Sánchez-Navarro V et al (2022) Long-term
compost amendment changes interactions and specialization in the
soil bacterial community, increasing the presence of beneficial
N-cycling genes in the soil. Agronomy 12:316. https://​doi.​org/​
10.​3390/​agron​omy12​020316
38. Chen F, Zhang J, Ji HJ et al (2021) Deinococcus radiodurans
exopolysaccharide inhibits Staphylococcus aureus biofilm forma-
tion. Front Microbiol 12:712086
13
972
39. Bali R, Pineault J, Chagnon PL, Hijri M (2021) Fresh compost tea
application does not change rhizosphere soil bacterial community
structure, and has no effects on soybean growth or yield. Plants
10:1638
40. Heisey S, Ryals R, Maaz TM, Nguyen NH (2022) A single appli-
cation of compost can leave lasting impacts on soil microbial
community structure and alter cross-domain interaction networks.
Front Soil Sci 2:749212
41. Kim MJ, Shim CK, Kim YK et al (2015) Effect of aerated compost
tea on the growth promotion of lettuce, soybean, and sweet corn
in organic cultivation. Plant Pathol J 31:259–268
42. Lutz S, Thuerig B, Oberhaensli T et al (2020) Harnessing the
microbiomes of suppressive composts for plant protection: from
metagenomes to beneficial microorganisms and reliable diagnos-
tics. Front Microbiol 11:1810
43. Ayankojo IT, Morgan KT, Kadyampakeni DM, Liu GD (2020)
Tomato growth, yield, and root development, soil nitrogen and
water distribution as affected by nitrogen and irrigation rates on a
Florida sandy soil. HortScience horts 55:1744–1755
44. Marchi EC, Zotarelli L, Delgado JA, Rowland DL, Marchi G
(2016) Use of the nitrogen index to assess nitrate leaching and
water drainage from plastic-mulched horticultural cropping sys-
tems of Florida Intl. Soil Water Conserv Res 4:237–244
45. Zotarelli L, Scholberg JM, Dukes MD, Muñoz-Carpena R (2007)
Monitoring of nitrate leaching in sandy soils: comparison of three
methods. J Environ Qual 36(4):953–962
46. Brust GE (2019). Management strategies for organic vegetable
fertility. In Safety and practice for organic food (pp. 193–212).
Academic Press.
47. Berg G, Rybakova D, Fischer D et al (2020) Microbiome defi-
nition re-visited: old concepts and new challenges. Microbiome
8:103
48. Minamisawa K, Nishioka K, Miyaki T et al (2004) Anaerobic
nitrogen-fixing consortia consisting of clostridia isolated from
gramineous plants. Appl Environ Microbiol 70:3096–3102
49. Miyamoto T, Kawahara M, Minamisawa K (2004) Novel endo-
phytic nitrogen-fixing clostridia from the grass Miscanthus
13
M. G. Martínez‑Yáñez et al.
sinensis as revealed by terminal restriction fragment length poly-
morphism analysis. Appl Environ Microbiol 70:6580–6586
50. Bageshwar UK, Srivastava M, Pardha-Saradhi P et al (2017)
An environmentally friendly engineered Azotobacter strain that
replaces a substantial amount of urea fertilizer while sustaining
the same wheat yield. Appl Environ Microbiol 83:e00590-e617
51. Li X, Wang X, Shi X et al (2020) Compost tea-mediated induction
of resistance in biocontrol of strawberry Verticillium wilt. J Plant
Dis Prot 127:257–268
52. Zhang J, Cook J, Nearing JT, Zhang J et al (2021) Harnessing the
plant microbiome to promote the growth of agricultural crops.
Microbiol Res 245:126690
53. Neher DA, Weicht TR, Bates ST et al (2013) Changes in bacte-
rial and fungal communities across compost recipes, preparation
methods, and composting times. PLoS ONE 8:e79512
54. Kalam S, Basu A, Ahmad I et al (2020) Recent understanding
of soil acidobacteria and their ecological significance: a critical
review. Front Microbiol 11:580024
55. Lidbury IDEA, Borsetto C, Murphy ARJ et al (2021) Niche-adap-
tation in plant-associated Bacteroidetes favours specialisation in
organic phosphorus mineralisation. ISME J 15:1040–1055
56. Mujakić I, Piwosz K, Koblížek M (2022) Phylum gemmatimon-
adota and its role in the environment. Microorganisms 10:151
57. Luo Y, van Veelen HPJ, Chen S et al (2022) Effects of sterilization
and maturity of compost on soil bacterial and fungal communities
and wheat growth. Geoderma 409:115598
58. Lau SE, Teo WFA, Teoh EY et al (2022) Microbiome engineer-
ing and plant biostimulants for sustainable crop improvement and
mitigation of biotic and abiotic stresses. Discov Food 2:9. https://​
doi.​org/​10.​1007/​s44187-​022-​00009-5
Springer Nature or its licensor (e.g. a society or other partner) holds
exclusive rights to this article under a publishing agreement with the
author(s) or other rightsholder(s); author self-archiving of the accepted
manuscript version of this article is solely governed by the terms of
such publishing agreement and applicable law.