Enhancement of Cellulose Rich Organic Matter Degradation
by Inoculation with Streptomyces sp. Strains
Simonida Djurić1,
Timea Hajnal-Jafari1*, Dragana
Stamenov1, Dejan Vidanović2,
Vuk Vračar1 and Biljana Najvirt1
1Faculty of Agriculture, University of Novi Sad, Novi
Sad, Serbia
2Veterinary
Specialist Institute “Kraljevo”, Kraljevo,
Serbia
*For
correspondence: mikrobiologija@polj.uns.ac.rs
Received 09 February 2021; Accepted 23 April 2021; Published 10 July 2021
Abstract
Microbial degradation of organic matter is a vital part
of carbon cycle in nature. Actinobacteria play an important role in the
decomposition of cellulose rich organic matter (CROM). Streptomyces spp. are abundant in soil, produce various secondary
metabolites and secrete extracellular enzymes. The aim of this research was to
isolate and select Streptomyces
strains with the best cellulose degradation abilities. Out of total 32
actinobacteria isolates, four Streptomyces
strains (CA1, CA10, PA2 and PA7) were subjected to morphological, physiological,
biochemical characterization and molecular identification.
CROM degradation potential of the strains was investigated on straw and beech
briquettes as well as on legume
based substrate in in vitro condition. Streptomyces strains CA1 and CA10 showed
the best cellulose production and starch hydrolysis abilities, followed by
strains PA2 and PA7. Strain CA1 was also positive to production of pectinase
enzymes. Streptomyces zaomyceticus
CA1 and S. tanashiensis
CA10 were used as inoculants, which degraded the raw cellulose from 38.38 to
81.69% in the investigated substrates (straw, beech, legume), during a 30-day
incubation experiment. CROM inoculation with the selected Streptomyces strains improved and accelerated its degradation in
controlled conditions. © 2021 Friends Science
Publishers
Key words: Cellulose
degradation; Actinobacteria; Streptomyces
sp.; Inoculation; Enzymes
Introduction
Cellulose is a major component of plant biomass and the
most common organic compound on earth (Gonzalo et al. 2016). By chemical
composition, cellulose is a linear polysaccharide composed of glucose molecules
connected with β 1‒4 glycosid bonding (Hussain et al. 2017). Plants produce 4×109 tons of cellulose per
year (Abedin 2015). The remains of crops rich in cellulose make up 50% of the
agricultural organic matter dry mass, whose microbial degradation is a vital
part of carbon cycle in the biosphere. The decomposition of that biomass is
done by cellulolytic bacteria, fungi and actinobacteria (Haruta
et al. 2002). Microorganisms produce
hydrolytic enzymes called cellulases, a complex of three important enzymes that
act synergistically thanks to the crystalline and amorphous complex structure
of cellulose. These enzymes hydrolyze cellulose into cellobiosis,
glucose and oligo-saccharides.
Actinobacteria play an important role in the degradation
of cellulose rich organic matter. About 90% of the total population of
actinobacteria is species of the genus Streptomyces
(Poopal and Laxman 2009). Streptomyces are slowly growing filamentous bacteria, abundant in
soil, but also in environments with harsh conditions since they are highly adaptable
due to their thermo tolerance and spore forming ability. The genus is mainly
known and researched for their production of various secondary metabolites such
as antibiotics and volatile compounds (Elardo et al. 2009). But they also secrete
extracellular enzymes (cellulases and proteases). Cellulose-degrading activity
was found in the genus Streptomyces
in various species and strains (Prasad et
al. 2013; Devi et al. 2018).
Research of Berlemont and Martiny
(2013), aimed at genomic analyses of 5,123 bacterial genomes from 8 major phyla.
It was demonstrated that nearly all Streptomyces
genomes contained Carbohydrate-Active Enzymes (CAZy).
Many authors showed that Streptomyces
could be a source of CAZy and used in various enzyme based technologies (Saratale
et al. 2012; Soeka
et al. 2019). However, the
introduction or Streptomyces strains
to organic matter in order to enhance its decomposition is not enough
investigated. Zhao et al. (2017)
showed that inoculation of compost with Streptomyces
strains H1, G1, G2, and Actonobacteria
T9, at different stages improved cellulase activities and accelerated the
degradation of cellulose. Streptomyces
albus BM292 exhibited great potential for bioaugmentation of compost
(Jurado et al. 2014). Olson
et al. (2012) also argued that
actinobacteria could be used as inoculants in which cellulose was degraded into
desired products.
Therefore, the aim of this research was to isolate and
select Streptomyces strains with good
cellulose degrading abilities. Moreover, another object of the study was to
evaluate the CROM degradation potential of the selected strains on different
cellulose rich substrates in in vitro
condition.
Materials and
Methods
Isolation of Streptomyces strains
Microorganisms were isolated from soil pseudogley (locality village Maovi
near Šabac – Pocerina: N
44˚41’43,73’’; E 19˚37’31,04’’) having the following characteristics:
1.67% CaCO3; 5.19% humus; 0.26% N; 177.5 mg P2O5 in
100 g of soil; 105.34 mg K2O in 100 g of soil; pH in H20
6.78; pH in KCl 5.80.
A 10 g of soil sample was suspended in 90 mL of 0.1 M
MgSO4×7H2O buffer and shaken for 10 min at 180 rpm on a
rotary shaker. The soil suspension was then diluted in four-fold steps in glass
tubes to an end point dilution of 10-5. 100 µL of the dilutions
(10-1
to 10-5) were spread onto Synthetic agar (glucose 10 g L-1,
NaNO3 10 g L-1, K2HPO4 10 g L-1,
KCl 10 g L-1, MgSO4 × 7H2O
10 g L-1, agar 15 g L-1), and incubated at 28ºC for 7‒10 days. Powdery colonies which were established as
gram-positive, filamentous bacteria that form a branching network of filaments
and produce spores were picked.
Physiological
and biochemical characterization of Streptomyces
isolates
To determine the carbon source utilization, isolates were
grown on Hugh-Lifsson medium (pepton
2 g L-1, HP 0.3 g L-1, NaCl 5 g L-1,
carbon source 10 g L-1, brom-thymol blue
0.03 g L-1, agar 3 g L-1) with different carbon source
(glucose, fructose, lactose, sucrose, xylose). The change in color, from green
to yellow, indicated a positive reaction.
The isolates ability to grow at
different temperatures (5, 15, 28, 37 and 45°C), on substrates of different
acidity (pH 5, 7 and 9) and on substrates with different NaCl concentrations
(3, 5 and 7%) were monitored on potato dextrose agar (PDA). The isolates were
incubated for 7 days. The diameter of the isolates
colony was measured and compared with the control.
The selected isolates were tested for their resistance
to antibiotics (penicillin 10 µg mL-1, novobiocin 5 µg mL-1,
tetracycline 30 µg mL-1, chloramphenicol 30 µg mL-1) by
disk-diffusion method (Amna et
al. 2019). After seven days of incubation at 28°C, the results were
recorded by measuring the diameter of the inhibition zone around the disks.
Completely tolerant isolates were denoted by “-no zone; + zone of inhibition of 0‒2 mm; ++ zone of inhibition of 2‒5 mm.
In vitro assay of extracellular
enzymatic activities
Production of pectinase was tested by the method of agar
plates on pectin agar. Incubation lasted 24 h at 37°C, after which colonies were
overflowed with lugol. The appearance of uncolored
zones around the colony was the evidence of pectinase activity (Soriano et al. 2000; Soares et al. 2001). Cellulase production was performed by flooding a
solution of Congo-red (1 mg cm-3 H2O) on isolates grown
on CMC agar (Kasing 1995). The presence of halo zone
around the colony was the proof of the cellulose decomposition. Starch
hydrolysis was assayed on starch agar, following the protocol as reported by
Cappuccino and Sherman (1992).
Urea degradation was tested on Christensen's urea agar (meat peptone 1 g L-1, dextrose 1 g L-1,
NaCl 5 g L-1, Na2HPO4 1.2 g L-1, KH2PO4
0.8 g L-1, phenol-red 0.012 g L-1, agar 15 g L-1,
urea 20 g L-1). The appearance of the reddish color in the medium
indicates the ureolytic activity of the isolate.
Lipase production was examined on medium (pepton 10 g
L-1, NaCl 5g L-1, CaCl2 × O 0.1 g L-1, agar 15 g L-1)
with Tween 80 addition. Formation the turbid zones around the colony are
evidence of lipolytic activity. Hydrolysis of gelatin was tested on deep
gelatinous agar (meat extract pepton broth (MPB) + 10‒15% gelatin) (Aneja 2003). After
incubation, degradation of gelatin in inoculated tubes was proof of the
gelatinase activity.
Streptomyces
isolates were screened for PGP activities on hydrogen cyanide (HCN) induction
medium (Tryptic Soy Broth 30 g L-1, Glycine 4.4 g L-1,
agar 15 g L-1), chrom-azurol S (CAS) medium and tryptone broth (containing 5 mmol L−1
tryptophan) for HCN, IAA and siderophores production, respectively (Schwyn and Neilands 1987; Frey-Klett et al.
2005; Etesami et al. 2015).
Molecular
identification
Actinobacteria DNA extraction was performed using the
Gene MATRIX Gram Plus and Yeast Genomic DNA Purification Kit (EURx Ltd.80‒297, Gdansk
Poland). The amount of DNA from four actinobacteria samples was determined on a
QFX Fluorometer apparatus (Denovix Inc, Wilmington,
USA). 16s rRNA gene sequences were obtained using two universal actinobacteria
primers. The first primer pair was 27F AGAGTTTGATCMTGGCTCAG 1492R
GGYTACCTTGTTACGACTT, while the second primer pair was S-C-Act-0235-a-S-20
GGCCTATCAGCTTGTTG S-C-Act-0878-a-ACG CCGG. After sequencing, two 1300
nucleotide length sequences and two 600 nucleotide length sequence were
obtained. Further identification was performed using the BLAST algorithm into
which the sequences were inserted (http://www.ncbi.nlm.nih.gov/genbank/).
Incubation
experiment
The incubation
experiment was performed on three different sources of organic matter – straw
briquettes, beech briquettes, and legume mix (containing six different beans
and peas’ varieties mixture). The amount of different
fractions in investigated substrates is presented in Table 1.
The substrates
were sterilized in autoclave (1 h at 121oC). 10 g of each substrate
were measured and placed in sterile Petri dish (9 cm diameter). The treatments
were: 1. Control (water); 2. S. zaomyceticus CA1; 3. S. tanashiensis
CA10. Each treatment contained three repetitions. A seven days culture of both strains was used. Spores were counted in
the Neubauer chamber, and their number was calculated in 1 mL of liquid
nutrient medium. By adding saline, the number was brought to 106
spores in 1 mL of inoculums and 10 mL was used per treatment, respectively.
The incubation
experiment lasted 30 days in controlled conditions (constant temperature 25oC,
moisture content was maintained at 60% field capacity). The amount of crude
cellulose was determined by the filter bags method (Page et al. 1982) on the ANCOM 2000 apparatus. The
percentage of crude cellulose was calculated using the formula:
% crude cellulose = 100 × (W3 -
(W1 × C1) / W2
Where W1 is the mass of the filter bag; W2 represents
the mass of the sample; W3 is the mass of organic matter and C1 is the
content-based correction factor.
Statistical analyses
The
incubation experiment was conducted in a completely randomized block design
with three replications. The data were subjected to analysis of variance
(ANOVA) to evaluate the efficiency of Streptomyces strains application.
The least significant difference test (Fisher LSD) was performed to compare the
results between treatments at P > 0.05. Software Statistica,
version 13.3 (TIBCO Software Inc.) was used for statistical analysis.
Results
Total 32 actinobacterial
isolates were isolated. Based on colony morphology, color, size and appearance
isolates were grouped. The isolates with whitish, compact, large to gigantic
colonies with wavy edges were designated as possible Streptomyces isolates (11 isolates). Further microscopic
observation proved the Gram positive, filamentous spore forming cells in four
isolates with numbers CA1, CA10, PA2 and PA7. Those isolates were chosen for
further physiological, biochemical characterization and genetic identification.
Physiological characterization of Streptomyces
strains
To
characterize the growth conditions, the selected strains were grown at the
specified temperature (5‒45°C), pH (5‒9), and NaCl concentrations (3‒7%). Several C source (five sugars) and antibiotics were
used to test C utilization and resistance, respectively (Table 2). The results
showed that the best temperatures for growth were between 28°C to 37°C for all
four Streptomyces strains. They grew
well in neutral pH but also in highly alkaline medium, except strain PA7,
indicating its quite wide pH tolerance. It was also found that the strains were
not grown even at the lowest tested NaCl concentration (except CA1), suggesting
that the strains might be halophobic. CA1 and PA7
used lactose and sucrose as C source, respectively. Only CA10 showed lack of
antibiotic resistance towards tetracycline, penicillin and chloramphenicol.
Biochemical characterization of Streptomyces
strains
Streptomyces strains CA1 and CA10 showed the best cellulose production and starch
hydrolysis abilities, followed by strains PA2 and PA7 (Table 3). All four
strains were weakly positive to urease test, and also to lipase production. Production
of HCN is important for plant pathogen suppression. Only strain PA2 proved
negative.
Molecular
identification
Table 1:
Basic chemical composition of the substrates - fresh mass (g 100 g-1)
Substrates |
Dry
matter |
Moisture |
Raw
cellulose |
Ash |
Straw
briquettes |
92,06 |
7,94 |
39,40 |
7,06 |
Beech
briquettes |
92,26 |
7,74 |
55,63 |
1,04 |
Legume
mix |
91,81 |
8,19 |
29,65 |
8,85 |
Table 2:
Physiological characterization and growth conditions
Growth conditions |
Strain number |
|||
CA1 |
CA10 |
PA2 |
PA7 |
|
Temperature (°C)* |
||||
5 |
- |
- |
- |
- |
15 |
+ |
+ |
- |
- |
28 |
++ |
++ |
++ |
+ |
37 |
++ |
++ |
++ |
++ |
45 |
- |
- |
- |
- |
pH* |
||||
5 |
- |
++ |
++ |
- |
7 |
++ |
++ |
++ |
+ |
9 |
++ |
++ |
+ |
- |
NaCl concentration (%)* |
||||
3 |
+ |
- |
- |
- |
5 |
- |
- |
- |
- |
7 |
- |
- |
- |
- |
C source* |
||||
Glucose |
- |
- |
- |
- |
Fructose |
- |
- |
- |
- |
Lactose |
+ |
- |
- |
- |
Sucrose |
- |
- |
- |
+ |
Xylose |
- |
- |
- |
- |
Antibiotics resistance** |
||||
Penicillin 10 µg mL-1 |
- |
+ |
- |
- |
Tetracyclin 30 µg mL-1 |
- |
++ |
- |
- |
Novobiocin 5 µg mL-1 |
- |
- |
- |
- |
Chloramphenicol 30 µg mL-1 |
- |
+ |
- |
- |
*-negative; + weakly positive; ++ positive
**-no zone; + zone of inhibition of 0–2 mm; ++ zone of
inhibition of 2–5 mm
Table 3: Biochemical
properties of Streptomyces strains
Biochemical properties |
Strain number |
|||
CA1 |
CA10 |
PA2 |
PA7 |
|
Pectinase test |
+ |
- |
- |
- |
Cellulase production |
+++ |
+++ |
+ |
+ |
Starch hydrolysis |
+++ |
+++ |
+ |
+ |
Urease test |
+ |
+ |
+ |
+ |
Lipase production |
+ |
+ |
+ |
+ |
Gelatin hydrolyses |
- |
- |
- |
+ |
Production of HCN |
+ |
+ |
- |
+ |
IAA production |
- |
+ |
- |
- |
Siderophore production |
- |
- |
- |
- |
-negative; + weakly
positive; ++ positive; +++ strongly positive
All
four actinobacterial samples were sequenced with two pairs of nucleotides to
obtain a sequence of about 1,300 nucleotides in length. After sequencing, two
isolates (PA2, CA10) obtained this length, while in PA7 and CA1 isolates, about
600 nucleotides were obtained, which was quite enough to perform the
identification up to species level.
CA1 isolate obtained 608 nucleotide sequences. Based on
the comparison with the existing sequences from BLAST, the isolate belonged to S. zaomyceticus.
CA10 isolate obtained 1372 nucleotide sequences. Based on the comparison with
the existing sequences from BLAST, the isolate belonged to S. tanashiensis. PA2 isolate obtained
1347 nucleotide sequences. Based on the comparison with the existing sequences
from BLAST, the isolate belonged to S. ambofaciens. PA7 isolate obtained 633 nucleotide
sequences. Based on the comparison with the existing sequences from BLAST, the
isolate belonged to S. zaomyceticus.
Incubation experiment
Thirty-day
incubation experiment showed that the amount of raw cellulose in the
investigated substrates decreased in all treatments (Table 4).
Percent decrease of the raw
cellulose content varied among treatments (Table 5). In straw briquettes
treated with S. zaomyceticus
CA1, the decrease compared to the amount at the beginning of the experiment was
69.65% while this reduction was 65.89% with the addition of S. tanashiensis
CA10. By adding S. zaomyceticus
to the beech based substrate, after a month of
incubation, there was a 51.57% decrease in the amount of cellulose compared to
the initial stage. S. tanashiensis
also reduced the cellulose content by 56.49%. In the legume-based substrate, the amount of raw cellulose was reduced by 81.32% after the
addition of S. zaomyceticus CA1 (Fig. 1). S. tanashiensis
CA10 decreased the amount of cellulose by 64.2% compared to the initial state.
Discussion
The Streptomyces strains were mesophylic, typical for the agroecological conditions of
the region they originated from. This is in accordance with the research of
Stamenov (2013), who determined that the optimal temperatures for
actinobacteria growth were between 28 and 37°C, while no isolate grew at 3 and
45°C. Sreevidya et
al. (2016) showed that four actinobacterial isolates grew on temperatures
between 20 and 40°C and pH ranging between pH 7‒11. Our research showed that the tested strains were
neither particularly good users of sugars (lactose by CA1 and sucrose by PA7)
nor did they grow in medium with added NaCl (only CA1 grew at 3% NaCl). Those
results are in contrast to those of Stamenov et al. (2016), who concluded that the Streptomyces isolates used glucose, galactose, fructose, sucrose, lactose
and xylose as C source and grew in media with elevated salinity (added 3‒7% NaCl). On the other hand, Dhanasekaran
et al. (2009) found that Streptomyces DPTD-5 and S. bikiniensis
used sucrose, lactose and fructose as carbon source. Antibiotic resistance test
singled out only strain CA10 as susceptible towards antibiotics. In the work of
Koushalshahi et
al. (2012) noted differential sensitivity of Streptomyces isolates towards seven antibiotics including
nitrofurantoin, nalidixic acid, gentamycin, erythromycin and rifampicin, while
they were resistant to penicillin and ampicillin.
Our research showed that actinobacteria strains produced
many extracellular enzymes, which participated in the mineralization of
investigated organic matter. All four strains produced cellulase, amylase and
lipase enzymes while one produced pectinase (CA1) and gelatinase (PA7). Aly et al. (2012) found that 20 out of 33
isolates of the genus Streptomyces
sp. produced lipases. On the other hand, Dhanasekaran
et al. (2009) found only one isolate,
out of 20 to perform hydrolysis of lecithin, lipids, pectin and starch, which
is in accordance with our results. Gopalakrishnan et al. (2011) also noticed that two of the five investigated
actinomycetes produced cellulase and protease enzymes. Research by Alam et al.
(2004) determined that different Streptomyces
strains were capable of producing cellulolytic enzymes during growth on various
cellulose substrates.
Statistically significant decomposition was achieved by
addition of Streptomyces strains,
though decrease of cellulose content in the watered treatment ranged between
24.23% in straw briquettes and 44.43% in beech briquettes. Those results could
be attributed to the process of cellulose natural decomposition which occurs at
a very low rate under normal atmospheric conditions (Jeong
et al. 2012). Thus, little is known
about water solubility of cellulose and the reactions needed to break the
hydrogen bonds which stabilize the structure of cellulose (Levi et al. 2016). It was demonstrated that S. zaomiceticus CA1
and S. tanashiensis
CA10 were particularly good producers of both cellulases and amylases. The
results obtained after the one month incubation
experiment with CA1 and CA10 strains, showed that the amount of raw pulp
decreased between 51.7% (from 554.4 to 268.5 mg g-1) to as much as 81.69% compared to the
initial state (295.5 compared to 55.2 mg g-1). This
coincided with the results obtained of Zhao et
al. (2017), who showed accelerated degradation of cellulose by
microorganisms. They added cellulolytic thermophilic actinobacteria to manure
and corn straw at different periods (several inoculations during decomposition)
and showed that inoculation led to an increase in cellulolytic enzymes
activity, accelerated the degradation of cellulose, increased the content of
humus substances and changed the structure of the actinobacteria community. In
the work of Zhao et al. (2016)
chicken manure was inoculated with Streptomyces
sp. and Micromonospora
sp during composting by different methods of
inoculation. The inoculation significantly accelerated the degradation of manure,
especially the cellulose fraction, which is consistent with the results of our
research. Maximum reduction of raw cellulose content was achieved after
inoculation of legume mix substrate with S.
zaomyceticus CA1. In this perspective, Sanchez et al. (2017) concluded that it is
necessary to develop technologies that should aim at improvement of the
nutritional characteristics of compost. By the addition of nutrients from
natural sources as well as microorganisms, the concentration of nutrients in
compost that are available to plants could be increased. Varma et al. (2017) after a study on the
microbial population involved in the degradation of ligno-cellulose
during the composting of mixed organic waste (e.g.
plant waste, manure fertilizer, dry leaves) concluded that combinations of
waste materials had a great influence on microbial degradation of waste
material and quality of final compost, due to their physical properties.
Heterotrophic bacteria were predominantly active during the initial composting
phase due to available organic matter, while actinobacteria were active during
the degradation of lingo-cellulose fractions.
Conclusion
Table 4:
Cellulose content in investigated substrates (mg g-1)
Substrate |
Initial state |
øH2O |
CA1 |
CA10 |
Straw briquettes |
392.1b* |
297.1k |
119.0h |
133.7g |
Beech briquettes |
554.4a |
308.1c |
268.5d |
241.2e |
Legume mix |
295.5k |
165.2f |
55.2j |
105.8i |
*Different letters
in subscripts indicate statistically significant difference according to Fisher
LSD test (p<0.05)
Table 5:
Decrease of raw cellulose content compared to
the initial state (%)
Substrate |
øH2O |
CA1 |
CA10 |
Straw briquettes |
24.23 |
69.65 |
65.9 |
Beech briquettes |
44.43 |
51.57 |
56.49 |
Legume mix |
44.1 |
81.32 |
64.2 |
Fig. 1: Substrate of
legume mix: control (a) and treatment with S.
zaomyceticus CA1 (b), 30 days after inoculation
S. zaomyceticus CA1 and S. tanashiensis CA10, decreased the amount of the raw
cellulose between 38.38 and 81.69% in all three investigated substrates (straw,
beech, legume), during a 30 day incubation period. The
selected strains showed a potential to promote the degradation of cellulose in
the substrates. Their
application in agriculture, as mineralization enhancer could speed up the
biodegradation processes of cellulose rich OM in soil. It could also help to
harvest different end products which are formed as a result of fermentation of
various materials and wastes rich in carbohydrates.
Acknowledgements
This work was supported by the Ministry of Education,
Science and Technological Development of the Republic of Serbia (Contract No.
451‒03‒68/2020‒14/200117).
Author
Contributions
SDj planned the experiments, THJ, DS and BN gathered and
interpreted the results, VV and DV did the molecular analyses. DS statistically
analyzed the data. SDj and THJ wrote the paper.
Conflicts of
Interest
All authors
declare no conflicts of interest
Data Availability
Not applicable in this paper
Ethics
Approval
Not applicable in this paper
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