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Critical Reviews in Biotechnology

ISSN: 0738-8551 (Print) 1549-7801 (Online) Journal homepage: https://www.tandfonline.com/loi/ibty20

Screening concepts, characterization and


structural analysis of microbial-derived bioactive
lipopeptides: a review

Piotr Biniarz, Marcin Łukaszewicz & Tomasz Janek

To cite this article: Piotr Biniarz, Marcin Łukaszewicz & Tomasz Janek (2017) Screening
concepts, characterization and structural analysis of microbial-derived bioactive lipopeptides: a
review, Critical Reviews in Biotechnology, 37:3, 393-410, DOI: 10.3109/07388551.2016.1163324

To link to this article: https://doi.org/10.3109/07388551.2016.1163324

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CRITICAL REVIEWS IN BIOTECHNOLOGY, 2017
VOL. 37, NO. 3, 393–410
http://dx.doi.org/10.3109/07388551.2016.1163324

REVIEW ARTICLE

Screening concepts, characterization and structural analysis of


microbial-derived bioactive lipopeptides: a review
Piotr Biniarza, Marcin Łukaszewicza and Tomasz Janeka,b
a
Faculty of Biotechnology, University of Wroclaw, Wroclaw, Poland; bDepartment of Inorganic Chemistry, Faculty of Pharmacy, Wroclaw
Medical University, Wroclaw, Poland

ABSTRACT ARTICLE HISTORY


Lipopeptide biosurfactants are surface active biomolecules that are produced by a variety of Received 1 April 2015
microorganisms. Microbial lipopeptides have gained the interest of microbiologists, chemists and Revised 21 December 2015
biochemists for their high biodiversity as well as efficient action, low toxicity and good biodegrad- Accepted 23 December 2015
ability in comparison to synthetic counterparts. In this report, we review methods for the produc-
KEYWORDS
tion, isolation and screening, purification and structural characterization of microbial lipopeptides. Biosurfactants; chemical
Several techniques are currently available for each step, and we describe the most commonly uti- analysis; lipopeptides;
lized and recently developed techniques in this review. Investigations on lipopeptide biosurfac- microbe; purification;
tants in natural products require efficient isolation techniques for the characterization and screening
evaluation of chemical and biological properties. A combination of chromatographic and spectro-
scopic techniques offer opportunities for a better characterization of lipopeptide structures, which
in turn can lead to the application of lipopeptides in food, pharmaceutical, cosmetics, agricultural
and bioremediation industries.

Introduction in cyclic LP. The best known cyclic LP are surfactins, itur-
ins, fengycins, lichenysins, viscosins, amphisins and puti-
Microorganisms produce a wide variety of chemical com-
solvins. Due to their chemical structure and biological
pounds. Some of these molecules are already exploited
and physiochemical properties, LPs are a particularly
in different fields, such as medicine and industry, while
others are likely waiting to be discovered and developed. promising class of BS.[2,3,6,7]
Among the thousands of microbial-derived compounds, LPs exhibit activities that make these molecules
biosurfactants (BS) are one such emerging class of mole- potentially useful in industry, environmental protection
cules.[1] BS are amphiphilic secondary metabolites that and medical fields. Previous research has highlighted
have surface and interfacial activity as every molecule their potential use as bioemulsifiers, heavy metal-bind-
contains both hydrophobic and hydrophilic moieties. ing compounds, antibiotics, antifungals and antitumor
Thus, BS are capable of reducing the surface tension or agents. Potential applications of LP/BS has been the
solubilizing hydrophobic substances in water. They are subject of a number of thorough reviews and research
considered to be ‘‘green’’ alternatives for chemical surfac- publications.[2,3,8–12]
tants that are widely used in different aspects of human The broad spectrum of properties attributed to LP can
activity, such as industry, farming and medicine.[1] be credited to their modularity, which results in a variety
BS are produced mainly by bacteria (e.g. Bacillus and of possible structures. A change in a single amino acid
Pseudomonas genera) and yeasts, such as Candida or within the molecule can cause an activity modifica-
Yarrowia [2–5] BS are a broad group of molecules that tion.[13,14] LPs are synthesized by macromolecular pro-
include lipopeptides (LP), lipoproteins, glycopeptides, tein complexes known as non-ribosomal peptide
phospholipids, etc. LP are comprised of a hydrophobic synthetases (NRPS). The modular organization of these
tail, which is usually a fatty acid, linked to a hydrophilic complexes and the possibility of rearrangement within
head between 4 and 12 amino acids. The hydrophilic the NRPS genetic clusters enables the production of a
head may be linear or contain a lactone ring as is found great variety of LP. The molecular basis of LP

CONTACT Tomasz Janek tomasz.janek@umed.wroc.pl Department of Inorganic Chemistry, Faculty of Pharmacy, Wroclaw Medical University, Borowska
211a, Wroclaw 50-552, Poland
Supplemental data for this article can be accessed here.
ß 2016 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives License (http://creativecommons.org/Licenses/by-nc-
nd/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited, and is not altered, transformed, or
built upon in any way.
394 P. BINIARZ ET AL.

biosynthesis has been extensively reviewed by many BS. Thus, it is likely that the distribution of BS producers
authors.[7,14,15] in different environments is underestimated.[33]
While some research teams have focused on the pro- According to our current knowledge, no metagenomic
duction, purification and characterization of already approach has been widely used for the screening of
known LP/BS,[16–19] others seek for innovative applica- BS-producing strains [35–38]. Such an approach could be
tions for BS.[8,11,20,21] The third branch of BS research designed for LP-producers due to the following: the high
is searching for novel molecules.[22–25] homology of NRPS operons in different species, the num-
The identification of novel LP is critical to enrich our ber of already designed primers in the literature and the
knowledge of BS and will provide researchers with mol- possibility of utilizing different databases and platforms,
ecules that may have desirable characteristics, such as like BLAST, NRPS predictor or AntiSMASH as exam-
high temperature stability, activity in a broad range of ples.[39–44] In our opinion, this may be the most cost-
pH and salinity levels, satisfactory biodegradability and/ effective and efficient way to analyze LP/BS produced by
or new biological activities.[2,26–28] microorganisms in different environments.
Although many valuable papers on BS have been After all, the isolation and cultivation of pure micro-
published, we found no concise review that introduced bial cultures must first be carried out before screening
and described a workflow of LP/BS research. The goal and/or other analyses.[36] Standardized microbiology
here is to outline the techniques that, in our opinion, protocols are often used to isolate and culture the
should be followed in a comprehensive study on novel microbes. First, samples are taken from a specific type
LP/BS, beginning from the isolation and screening of of source (e.g., water or soil), diluted and plated on vari-
BS-producing microbes, through the production and ous types of agar plates (Figure 1). After a few days of
purification of the novel compounds and finally, com- incubation, single colonies are selected and transferred
pound characterization. It is hoped that this review on to a liquid medium to cultivate individual microbes
LP can assist researchers whose studies are dedicated to separately.[17] As an alternative, enrichment culturing
LP but can also be applied to other classes of BS due to is a popular modification of this standardized
their similar physicochemical properties. approach.[33,45] In this technique, environmental sam-
ples are incubated in a liquid medium using hydrocar-
Isolation and screening of BS-producing bon as the main carbon source to promote the growth
microorganisms of hydrocarbon-degrading microbes. Samples taken
There are a variety of traditional, popular and recently from enrichment cultures are subsequently diluted and
developed methods for the isolation and screening of agar plated as previously described. The correlation
microbial BS producers. Some of these methods have between microbial growth on hydrophobic carbon sub-
been exhaustively tested and reviewed while others are strates and the production of BS has been reported,
rarely employed.[22,24,29,30] Thus, these techniques although researchers should keep in mind that there are
will not be discussed and instead, we will focus mainly always exceptions from every rule.[33]
on novel high-throughput methods. Recently, protocols for high-throughput isolation
The workflow of BS research begins with the isolation approaches have been published, but these techniques
of microorganisms followed by screening and identifica- are still in development.[46–48] We were unable to
tion of BS-producing strains (Figure 1). These microbes identify reports that described the utilization of high-
(e.g. bacteria, archaea and fungi) are isolated from envir- throughput isolation procedures followed by HTS for BS
onmental samples, such as soil and water, collected production; therefore in our opinion, this is a field worth
from around the world.[23,29,32,33] A small percentage developing. High-throughput isolation techniques also
of environmental isolates normally produce BS.[33] have the potential to assist with the cultivation of
Interestingly, this number can rise to 25% in samples currently ‘‘uncultivable’’ BS-producing microbes.[47]
from hydrocarbon or heavy metals-polluted sites or Therefore, these techniques can be useful for estimating
even more dramatically (up to 80%) when enrichment the distribution of BS producers in different niches as
cultures with hydrocarbons are used.[24,29,32–34,] well as uncovering ‘‘unknowns’’ of BS production.
All methods adopted for the screening of BS pro- When isolates are grown and single, pure colonies
ducers share an important limitation – only microbes are isolated, they can be screened for the production of
susceptible for artificial cultivation can be isolated and BS (Figure 1) with several highly utilized, traditional
analyzed. Moreover, the conditions and media used for techniques that involve direct and/or indirect methods
preliminary cultivation of the isolates can influence the (Table S1). But in a past few years, new screening proto-
metabolism of microorganisms and inhibit production of cols have appeared. We present the current knowledge
CRITICAL REVIEWS IN BIOTECHNOLOGY 395

Figure 1. Standardized workflow for the identification and characterization of BS/LP. BS-producing microbes can be found in envir-
onmental samples (A) and isolated with a variety of microbiological techniques (A1, B) to pure colonies (C). Next, microorganisms
are screened with one or more HTS techniques (e.g. drop collapse assay or its modifications) for the ability to produce BS (D). BS-
positive strains are then identified (e.g. by 16S rDNA sequencing; D1). Production of BS should be additionally confirmed (e.g. by
TLC; E). BS/LP can be produced in standard laboratory Erlenmeyer flask (F). To obtain a pure compound (G) that can be used in dif-
ferent examinations, several isolation/purification techniques can be used. A structure of pseudofactin II (H) is given as an example
of a LP molecule that passed through the presented workflow [10–12,31]

on these newly developed indirect (Table 1) and direct of microbial cultures (e.g. measuring surface tension
techniques (Table 2) below. during cultivation) and/or to detect emulsification activ-
All types of surfactants can be detected simultan- ity or antimicrobial/hemolytic activity of culture super-
eously with indirect screening methods,[22,25,30,51] natants.[26,54] Due to simplicity, indirect screening
while direct methods can usually be used for only one techniques are usually used for preliminary screening
type at a time.[56,57] Indirect methods can provide pre- for BS producers.[25,29] Specific techniques are
liminary information on BS production kinetics and described in Table 1 and Table S1.
yield. Although these methods may result in false posi- While indirect screening techniques are inexpensive
tive or false negative qualitative data as well as under- and easy to carry out, they have several disadvantages
or overestimating BS yields. The various indirect techni- (Table 1 and Table S1) and are being replaced by direct
ques also differ in sensitivity, and only some are suitable approaches (Table 2). The more sophisticated direct
for high-throughput screening (HTS). Moreover, these methods (Table 2) can answer several different ques-
results do not provide information on the nature and tions. Certain direct techniques can reveal additional
structure of any detected surface active compound(s). properties, such as structural information. The decision
Indirect screening methods (Table 1 and Table S1) tend as to which method would be the most suitable should
to be used to reveal changes in the surface properties be considered with a specific scientific question in
396

Table 1. Indirect, novel screening methods used for revealing BS-producing microbes. These HTS procedures can be used for detecting all types of surfactants and are mostly based
on measuring changes in the surface properties of examined sample
Application Quantitative
Method name Applicability Short description Simplicity in HTS Precision results Sensitivity Comments References
P. BINIARZ ET AL.

Modified drop-collapse BS Each well of 96-well microplate is þþþ þ þ þ þ One of the most utilized [22,49,50]
coated with thin layer of oil (e.g. min- methods for detection of BS,
eral oil) prior to analysis. Then a 5 ml together with a simple drop
drop of a sample is added to the cen- collapse analysis (cf. Table S1).
ter of a well and observed after
1 min. Presence of surfactants in solu-
tion will result in a larger diameter of
a drop in comparison to water drop.
Microplate meniscus BS 100 ml of microbial culture super- þþþ þþ þ þþ þ Rough quantitative results can [29]
shape assay natant is put into a 96-well micro- be obtained by diluting the
plate and diluted serially. Then, the sample serially on a micro-
plate is investigated – an image of a plate. Applied in a limited
grid is viewed through the plate. number of research works.
When surfactants are present in solu-
tion, the surface of a liquid in well
forms a concave lens which distorts a
view of a grid.
Atomized oil assay BS Microbial cultures are spotted on agar þþþ þ þ þþ þ Designed for uncovering sur- [45,50,51]
plate and grown. BS solution can be face-enhanced production of
also spotted on a plate. Then, a mist BS (yet, many strains produce
of mineral oil is applied on a surface BS only if grown in liquid
of agar with an airbrush. A halo media).
around BS spots or BS-producing
microbes can be observed and
measured.
Polydiacetylene (PDA) Surfactin/ionic PDA vesicles, which act as sensors for þþ þþ þþ þþ þþ Applied in a limited number [52]
vesicles surfactants surfactants, are synthesized from of research works.
PCDA (10,12-pentacosadiynoic acid).
Solutions containing BS and PDA
vesicles are mixed in microplate and
the color change is measured.
Simplicity is an outcome of availability and price of laboratory equipment and materials needed in a certain test as well as demand for skilled staff: very easy (þ þ þ), easy (þ þ), difficult (þ); application in HTS: very
good (þ þ þ), good (þ þ), poor (þ); precision is an outcome of repeatability of a certain test and the probability of receiving false-positive or false-negative results: very precise (þ þ þ), precise (þ þ), imprecise
(þ); quantitative results: very good (þ þ þ), good (þ þ), poor (þ), not applicable (); sensitivity is the relative concentration of surfactant that can be detected: very good (þ þ þ), good (þ þ), poor (þ), not applic-
able ().
Table 2. Direct, HTS and emerging methods designed for the fast and accurate detection of LP or LP-producing microorganisms
Application Quantitative
Method name Applicability Short description Simplicity in HTS Precision results Sensitivity Comments References
NRPS operon detection LP PCR reaction with primers designed þþþ þþ þþ   Detection of PKS (polyketide syn- [39,43,53,54]
with PCR for conserved regions of NRPS is thases) and/or silent NRPS
carried out. Purified microbial DNA operons is possible, what may
or ‘‘colony PCR’’ supernatant can lead to false-positive results.
be both used as a template for
PCR reaction. PCR products are
detected after agarose gel
electrophoresis.
HPLC/UPLC LP/BS Clarified culture supernatant or crude þþ þþþ þþþ þþþ þþ Expensive equipment and certain [17,54,55]
culture extract can be injected on laboratory skills are needed.
RP-HPLC/UPLC column (C18 is Samples should be analyzed
commonly used) and eluted with simultaneously with purified
water/ACN gradient. LP’s are standards for comparison.
detected at a wavelength of
approx. 210 nm. Identification of
eluted compounds can be done by
comparing the retention time or
second derivative of spectrum with
standards.
LC-MS Small molecular Methods are usually similar to HPLC/ þ þþþ þþþ þþþ þþþ Requires use of an expensive and [17,56,57]
mass BS UPLC analysis. The main difference sophisticated laboratory equip-
is the way of detection. Here, dif- ment, which should be oper-
ferent MS approaches/ionizations ated by skilled staff. Studies on
(e.g. ESI) are used and response of the structure of detected com-
MS detector is observed. pounds can be done simultan-
eously by the analysis of MS/
MS spectra.
MS-based approaches LP/BS Several different methods have been þ þþþ þþþ þ þþþ Requires an expensive or even in- [17,58,59]
(potentially) demonstrated e.g. nanoDESI (nano- house built, prototype equip-
spray desorption electrospray ion- ment and skilled staff. Huge
ization), MALDI-TOF (matrix- amounts of data are gener-
assisted laser desorption/ionization ated, what can cause problems
– time of flight) or other. Variety in selection and analysis of
of sample types can be analyzed essential information. Structural
(microbial colonies, microbial cul- data can be obtained
tures or culture supernatants, cul- simultaneously.
ture extracts).
PrISM (proteomic investigation LP Microbes are grown and subsequently þ þþ þþ   Technique is very similar in its [60]
of secondary metabolism) proteome samples are prepared. assumptions to PCR-based
Samples are loaded onto SDS- methods. Due to ‘‘protein-first’’
PAGE gel and high molecular strategy, probability of obtain-
bands (225 kDa) are isolated, ing false-positive results is
digested, and analyzed (LC-MS/MS) reduced (only expressed genes
for unique marker ions of NRPS can be detected). Experience in
and/or PKS enzymes. analysis of proteomic data as
well as expensive laboratory
equipment are essential.
CRITICAL REVIEWS IN BIOTECHNOLOGY

Simplicity is an outcome of availability and price of laboratory equipment and materials needed in a certain test as well as demand for skilled staff: very easy (þ þ þ), easy (þ þ), difficult (þ); application in HTS: very
good (þ þ þ), good (þ þ), poor (þ); precision is an outcome of repeatability of a certain test and the probability of receiving false-positive or false-negative results: very precise (þ þ þ), precise (þ þ), imprecise
(þ); quantitative results: very good (þ þ þ), good (þ þ), poor (þ), not applicable (); sensitivity is the relative concentration of surfactant that can be detected: very good (þ þ þ), good (þ þ), poor (þ), not applic-
397

able ().
398 P. BINIARZ ET AL.

mind. Direct methods developed for recognizing LP structural analysis of BS in a single experiment.[59] Such
include: PCR-based procedures [43,53,54] and several methods are, in our opinion, the future not only of LP/
extraction methods coupled with analytical techniques BS research but also analyses of different types of active
(Table 2). There are also newly-developed, high-through- biomolecules. On the other hand, MS-based procedures
put MS-based and proteomics approaches [59,60] that require sophisticated equipment, a highly-skilled staff
potentially could replace traditional screening techni- and the capability to analyze huge amounts of gener-
ques (Table 2). After certain modifications, these techni- ated data (Table 2).
ques can be also adapted for uncovering different LP research workflow can also begin with an in situ
classes of BS.[61] genome analysis. Whole microbial genomes or their
The screening step is critical for efficient BS research; fragments can be analyzed, or ‘‘mined’’ for the gene
thus, screening techniques require careful selection. clusters that encode NRPS operons. Until now, there
Each approach has its own merits and shortcomings have only been a few possible ways to detect NRPS
(Table 1, Table 2 and Table S1); therefore, we suggest a operons in situ (reviewed in. 62,63] The most obvious
two-part screening procedure as a successful and effi- method is to compare the nucleic acid sequence of
cient strategy (Figure 1). In the first step, a HTS tech- interest with known sequences using BLAST.[64,65]
nique would be used to screen a large number of However, more accurate tools that are tailored for LP
isolates with relatively high sensitivity and low probabil- are also available.[62,63] These tools can not only be
ity of receiving false positive or false negative results. used to detect potential NRPS operons in genomes but
The perfect HTS approach would provide results that also to predict the possible structure of detected com-
would also help assess BS activity, yield, or antimicrobial pounds, comparing them with known LP to forecast
activity for instance, so only promising candidate strains activity and to annotate novel compounds.[62,63]
will be selected for subsequent analyses. Drop collapse, The identification of selected microbes should be car-
various microplate assays, PCR- and MS-based methods ried out at the end of screening (Figure 1) as this know-
can be used for a large-scale screen of isolates. Since ledge can be helpful in following BS-workflow steps
none of them individually is the perfect technique, other (e.g. in the choice of optimal cultivation medium and
factors should be considered when choosing the conditions, see next chapter). Traditional API-testing is
method, including: researcher experience in microbio- time-consuming and expensive, so it will probably be
logical laboratory techniques, available laboratory equip- outdated in the characterization of environmental iso-
ment, the number of isolated microbes to be tested and lates. 16S rRNA sequencing is currently the most
the desired level of sensitivity and accuracy (Table 1, exploited method for this purpose.[17,32,34] Although
Table 2 and Table S1). novel, automated and high-throughput MS-based
During the second screening step, selected BS-posi- approaches have emerged recently with the potential
tive isolates should be tested further to confirm the pro- for identifying hundreds of microorganisms in a single
duction of BS, identify the specific type of BS produced experiment. Different MS techniques can be used to
and estimate BS yield and/or activity. Measurements of detect bacterial biomarkers (e.g. proteins, lipids, lipopo-
the surface tension or emulsification activity of clarified lysaccharides or low-mass molecules) with measure-
microbial cultures are commonly utilized assays for con- ments accomplished within minutes. Results can be
firming BS production and estimating BS activity and compared with databases (e.g. Bruker BioTyper or
yield, while extraction of BS followed by TLC is typically SARAMIS) to identify the bacteria of interest to the sub-
used for receiving general information on the structure species level. Although MS-based biotyping procedures
of active compounds (Table S1).[12,25,26,29,30] are primarily used in clinical microbiology, they are pre-
These approaches are now replaced by novel techni- dicted to displace biochemical and molecular biology
ques, from which different HPLC/UPLC, LC-MS or MS are techniques in microbe identification in the near
probably the most promising, due to high sensitivity, future.[66] Isolation and screening for BS-producers
accuracy and automation. Absorbance (e.g. at 210 nm) ends when selected strains are frozen and banked in a
or MS data can be used for detection and quantification laboratory culture collection in 80  C for further culti-
of LP and MS/MS spectra can be adapted for resolving vation and analysis of surface active compounds.
the structure of active compounds (Table 2). These
methods can be adopted for different types of BS (e.g.
Cultivation of microbes for the production
glycolipids).[55,54] Moreover, some of the novel MS-
of LP
based procedures (e.g. nanoDESI) have the potential to
be used as universal methods to join the HTS screening Once LP/BS-producing microbes have been isolated and
(Figure 1D) and confirmation (Figure 1E) steps with identified, the efficient production and purification of
CRITICAL REVIEWS IN BIOTECHNOLOGY 399

surface active compounds is crucial to characterize the final products (see following chapters).[12] However,
structure and function of novel LP/BS (Figure 1) and BS production in MSM can be relatively low.[71]
require the optimal culture medium and growth condi- The use of complex media has also been investigated
tions for efficient LP production. Optimization of with conflicting reports. Early studies suggested that
nutrients and culture condition for the production of BS production decreases when complex media is
LP/BS is a topic of great interest.[2,16,18,67–72] Here, used.[73,77,78] However, subsequent studies indicated
we focus on the main parameters that can affect the that LP production was suitable using a number of dif-
efficient production of LP by microorganisms. ferent complex media as well as industrial wastes. These
LPs are produced by different microbes, including included King’s B medium [50] Landy’s medium,[82]
several Bacillus and Pseudomonas strains [14,17,37] as corn steep liquor,[83] and glycerol waste from biodiesel
well as other genera.[4,17,34] Generally, cultivation pro- production.[27,74]
cedures designed for Bacillus and/or Pseudomonas have Optimal medium and cultivation conditions should
been successfully used for the cultivation and produc- be selected for each individual LP/BS producer to reach
tion of LP by other genera.[17] maximum productivity, although amounts of LP suffi-
Several factors have been previously reported to be cient for analyses (Figure 1) can also be obtained from
crucial for the biosynthesis of LP. These include: nutrient non-optimized cultures.[11,12] Screening for the optimal
composition (carbon and nitrogen sources), fermenta- medium is usually carried out in standard laboratory
tion temperature, pH and culture oxygenation.[4,71] Erlenmeyer flasks by changing one factor (e.g. carbon
There are general rules that should be followed for the source type or concentration) at a time [67].
efficient production of LP. First, the pH of the culture Oxygenation can be controlled through the adjustment
should be kept at a neutral level (6.0–7.0), as acidic pH of agitation speed or by using baffled flasks.[73] This
can inhibit the production of LP or cause their precipita- traditional, time-consuming methodology can be
tion.[71,73] Second, a correlation between BS produc- replaced with newly developed microbioreactors sys-
tion and microbial growth has been reported.[67,71,74] tems for HTS of optimal media and conditions [76] and/
Therefore, nutrients, especially carbon and nitrogen or mathematical modeling of BS production, such as
sources and culture oxygenation should not be limiting Plackett–Burmann screening or response surface
for bacterial growth, although some exceptions have methodology.[18,67,72]
been reported.[12,75,76] Third, media selection should The optimization process for the production of BS
be conducted due to reports that rich, complex media, involves the assessment of LP/BS production to allow
such as LB (Luria-Bertani) or NB (Nutrient Broth), may the determination of optimal conditions. The production
cause decreased LP production.[73,77,78] Fourth, of LP/BS tends to be frequently overestimated. Thus, it
microbe cultivation at 30  C seems to be optimal for is important to develop a reliable technique for the
most LP producers,[58] although some strains prefer quantification of the molecules in question.[84]
lower temperatures.[75] Finally, microbial culturing Quantitative techniques employed for LP/BS screening
should last long enough for the microorganisms to (e.g. HPLC analysis) can be successfully adapted to pre-
reach the stationary phase of growth when the produc- cisely quantify BS (Table 2). However, the use of semi-
tion of most BS is maximized.[67,74] quantitative methods in the initial stages of LP research
The selection of culture media is an important step in can usually provide sufficient data. Therefore, simpler
efficiently generating ample amount of LP/BS for ana- and cheaper methods could be used. Microplate menis-
lysis. Minimal mineral salt media (MSM) are commonly cus shape or atomized oil HTS assays are worth consid-
used for the production of BS.[12,79,80] The compos- ering (Table 1), especially if laboratory equipment access
ition of MSM varies in different reports but generally is an issue.
consists of buffered salts (e.g. K2HPO4, KH2PO4, NaCl,
KCl), a carbon source (e.g. glucose, sucrose, glycerol or
Isolation and purification of LP
hydrocarbons) and a nitrogen source (e.g. (NH4)2SO4,
NH4NO3, NH4Cl, or KNO3). Increased LP production has Successful production must be followed by efficient
been described in MSM supplemented with trace ele- purification (Figure 1) as pure compounds should be uti-
ments, such as divalent cations.[73,80] Small amounts of lized for structural or physical analyses. To obtain pure
complex additives, like yeast extract or protein digests, samples of the LP from culture broth, efficient isolation
can also be added to promote bacterial growth and LP techniques are required.[30] Thus, one important factor
production.[67,81] Simplicity is probably the most for determining the feasibility of a production process
important advantage of MSM as subsequent isolation on a commercial scale is the availability of suitable and
steps are more easily performed with higher purity of economic recovery and downstream procedures.
400 P. BINIARZ ET AL.

Table 3. Methods for recovering LP from cultivation broths and their advantages
Method type Method name Experimental approach Advantages References
Analytical-scale Solvent extraction LP dissolves in organic solvents due to Recovery and partial purification, [12,89]
methods the presence of hydrophobic part in reusable nature of organic
their molecules solvents;
Acid precipitation LP become insoluble at low pH values. This method is easy, inexpensive [90–92]
Crude BS can be precipitated and/or and readily available to recover
centrifuged crude BS such as LP;
Dialysis Difference in solute concentration; water Effective in isolation of micelles [93]
soluble extracellular compounds are biosurfactants, reusability, fast
purified by dialysis; the typical dialysis recovery;
session is usually eight or ten hours
overnight at 4  C
Ammonium sulfate precipitation LP are precipitated using (NH4)2SO4 Efficient in recovery and partial [94,95]
purification of crude BS;
Ion-exchange chromatography Charged LP are eluted from ion-exchange High purity, reusability, fast recov- [96]
resins with proper buffer ery; high-throughput
Solid phase extraction (SPE) The analyte in SPE is eluted in an non- Fast, one-step recovery, high level [97]
polar solvent, which disrupts the inter- of purity, reusability; high-
action of the analyte and the station- throughput
ary phase
Adsorption on polystyrene resins LP are adsorbed on polymer resins and Fast, one-step recovery, high level [88]
subsequently desorbed with organic of purity, reusability; high-
solvents throughput
Preparative-scale Membrane ultrafiltration LP form micelles at concentrations above There are many merits of ultrafil- [86,98,99]
methods the critical micelle concentration; tration: No need for chemicals
therefore, they can be separated from One-step recovery High level
other molecules in cultivation broth by of purity Simple automation;
sequential ultrafiltration high-throughput
Adsorption on wood-activated carbon LP are adsorbed on activated carbon High level of purity, reusability, [100]
cheap recovery from continu-
ous culture high-throughput
Foam fractionation In this method, foam is collected Cheap recovery from continuous [101–103]
(through fractionation column) and culture;
acidified with HCl down to pH 1.0–2.0
to precipitate LP, which can be
extracted with organic solvents

Efficient and high-throughput processing methods are methods are foam fractionation, which depends on the
needed for the maximum recovery of LP/BS. foaming capabilities of LP, adsorption-desorption on
Conventional and unconventional methods for the polystyrene resins and ion exchange chromatography.
recovery of LP have been reported in recent These procedures take advantage of BS properties, such
years.[85–87] as their surface activity or their ability to form micelles
The main advantage of isolation and purification or vesicles, and are particularly applicable for the large-
methods is their ability to operate in a continuous mode scale continuous recovery of extracellular BS from cul-
for recovering LP with high level of purity. A single ture broth. In addition, these methods can operate in a
downstream processing technique is often not enough continuous mode for recovering BS with a high level of
for the recovery and purification of LP/BS. In such cases, purity [105] to produce amounts on a commercial scale.
a multi-step recovery strategy using a sequence of con- The most widely used techniques are organic solvent
centration and purification steps is more effective. With extractions with chloroform and methanol, petroleum
such a multi-step recovery process, it would be possible ether, ethyl acetate, n-hexane and ether.[26,106,107]
to obtain LP/BS at any required degree of purity.[88] Recently, ethyl acetate has been successfully used to
The most common methods for the purification of recover LP produced by Pseudomonas [12,108] and
microbial LP include solvent extraction, ammonium sul- Bacillus.[89] This organic solvent can be used to substan-
fate precipitation, ultrafiltration and dialysis (Table 3). tially reduce recovery expenses and minimize environ-
One of the simplest methods for the recovery of LP is mental hazards.[109]
acid precipitation.[104] Acid precipitation is carried out
using concentrated HCl to lower the pH to 2.0, which
Identification, characterization and
neutralizes negative charges on LP, making them less
quantification of LP by various
soluble in the aqueous phase. The precipitated LP can
chromatographic and spectroscopic techniques
then be collected for analysis. This method is easy, inex-
pensive, and readily available to recover crude LP from There are many chromatographic techniques used to
cell-free supernatant. Other more commonly used characterize and quantify molecules, including thin layer
CRITICAL REVIEWS IN BIOTECHNOLOGY 401

chromatography (TLC), preparative TLC (PTLC), column individual components of the BS mixture. This technique
chromatography (CC) or modern semi-preparative/pre- is gaining popularity among various chromatography
parative HPLC. Each technique has its own strengths approaches and is usually the main choice for LP stud-
and weaknesses and should be selected based on the ies. The resolving power of HPLC is ideally suited to the
nature of the target compound, such as solubility, rapid processing of multi-component samples on both
charge, stability and molecular size. Taking these factors analytical and preparative scales. HPLC is generally per-
into account, the choice of chromatographic methods formed using C8 or C18 reverse-phase columns with a
and the stationary phases to be used are important for water/acetonitrile (ACN) gradient. Common detection
designing a purification system. methods for the samples collected from HPLC columns
Other efficient spectroscopic techniques have been are UV spectroscopy, measurement of refractive index,
utilized for investigations on LP, such as 1H and 13C fluorescence, electrical conductivity and MS.
nuclear magnetic resonance NMR; [110] Fourier trans- The use of HPLC has been reported in the character-
form infrared (FT-IR) spectroscopy [30] and MS, to char- ization, quantification and purification of
acterize and evaluate chemical and biological LP.[12,117–119] For example, purification of LP by HPLC
properties.[111] LC-MS has been the most widely was carried out by reversed phase (RP)-HPLC using a
used.[112] These techniques will be reviewed in the fol- semi-preparative C18 column and 0.1% trifluoroacetic
lowing sections. acid/methanol/H2O as a mobile phase. The elution was
monitored using UV detection at 214 and 280 nm. The
metabolites eluting as individual peaks were used for
Thin layer chromatrograpy
further MS characterization.[120] Recently, the structure
TLC separates compounds in a mixture and can be used of LP produced by Citrobacter and Enterobacter were
to determine the number of components in solutions, subjected to further characterization.[17] The LP sam-
identify these compounds and test their purity.[113] TLC ples were purified with a RP-HPLC C18 column and the
techniques can be used to detect BS production by sep- elution was also monitored by UV detection at 215 nm.
arating cell-free culture supernatants on silica gel plates The solvent system used was (A) 0.1% aqueous TFA and
and characterizing the chemical nature of BS.[30] TLC (B) ACN containing 0.1% TFA. The following gradient of
can also initially characterize BS as LP with selective solvent B was used to run the column: 0–60% for
developing reagents as LP appear as red spots in the 0–45 min, 60–80% for 45–55 min, and 80–100% for
presence of ninhydrin.[114] Furthermore, LP have spe- 55–60 min.
cific retention factor (Rf) values for every solvent or solv-
ent mixture. Rf values can be used in compound
Liquid chromatography – mass spectroscopy
identification by comparing the unknown sample with
(LC-MS)
Rf values of known LP. Several TLC systems are designed
for the analysis of LP (Table S2). LC and MS, when used in tandem, provide a unique
TLC is one of the most versatile techniques for the capability for rapid, cost-effective and quantitative
identification of natural surface active compounds pro- measurements of organic molecules in an enormous
duced by microorganisms. It can also be used for moni- variety of applications. Coupling LC with MS provides
toring the quality and purity of raw BS extracts. Due to the advantages of characterizing retention time of a
the fact that BS extracts usually occur as a combination given LP/BS along with its mass spectral signature,
of various types of surface active compounds, their sep- allowing the analysis of complex mixtures. This is nor-
aration still remains a big challenge, as only pure com- mally achieved by splitting the HPLC eluent to convey a
pounds can be used for the process of identification fraction of the eluent into the mass spectrometer.[1]
and characterization.[58,107,115] It is a common prac- Direct analysis of LP/BS in fermentation broths using LC-
tice in the isolation of LP that multiple separation tech- MS is possible, but it is usually necessary to perform ini-
niques, such as TLC and PTLC are used to obtain pure tial steps of purification to remove the worst interfer-
compounds.[116] ences and also to concentrate the sample if BS is only
present at very low concentrations. The most important
and widely used LC separation technique for quantita-
High-performance chromatography (HPLC)
tive LC-MS is RP separation. This utilizes differences in
HPLC is a specific form of column chromatography used hydrophobicity (termed ‘‘nonspecific hydrophobic inter-
in chemical and biochemical analysis. HPLC is a tech- actions’’) to achieve partitioning between an apolar sta-
nique that can separate a mixture of surface active com- tionary phase and a polar mobile phase. Typically,
pounds and is used to identify, quantify and purify mobile phases are different blends of water with a
402 P. BINIARZ ET AL.

Table 4. HPLC solvent systems and MS approaches designed for the analysis of LP produced by microorganisms. Solvent mixtures
compositions are shown in volume ratios
MS method/
Biosurfactant Column Solvent system, flow rate RT from HPLC (min) ionization References
Surfactin Fengycin Analytical Luna 5 lm C18, (A) water, 1% formic acid; (B) ACN; C13 surfactin 18.89 [87]
A Fengycin B 150 mm  4.6 mm linear gradient A:B (50:50) for 3 min, C14 surfactin 20.06 ESI-MS
then A:B (0:100) over 18 min and C15 surfactin 20.06 [M þ H]þ
then 100% B over 5 min; flow rate of C14 fengycin A 3.80 [M  H]
0.8 mL/min C15 fengycin A 5.00 [M þ Na]þ
C16 fengycin A 6.50
C17 fengycin A 7.49
C14 fengycin B 4.94
C15 fengycin B 6.24
C16 fengycin B 7.41
C17 fengycin B 8.18
Lichenysin RRHD Zorbax Eclipse Plus (A) 2 mm ammonium acetate and ND ESI-MS [56]
1.8 lm C18 column, 0.2% heptafluorobutyric acid in water; [M þ H]þ
100 mm  2.1 mm (B) ACN and methanol (1:1); linear [M þ Na]þ
gradient from 90 to 93% B in 4 min,
8 min analysis time; flow rate
0.4 ml/min
Norsurfactin TOSOH TSKgel ODS- (A) distilled water with 0.1% formic ND ESI-MS [112]
Fengycin Iturin A 100 V 5 lm column, acid; (B) ACN containing 0.1% formic [M þ H]þ
Mixirin Pumilacidin 250 mm  4.6 mm acid; linear gradient from 3 to 97% B
Surfactin during 45 min; flow rate 0.5 mL/min

Iturin Surfactin Zorbax 300SB 5 mm ACN:water, both with 0.1% formic ND ESI-MS [121]
C18 column, acid as mobile phase solvents with ESI-MS/MS
150 mm  4.69 mm a 40 min linear gradient of 50–95% [M þ H]þ
ACN at 0.2 mL/min flow rate [M þ Na]þ
Bacillomycin F C18 reverse phase (RP) Linear gradient of deionized water ND ESI-MS [94]
column and ACN (0–100%) containing 0.05% ESI-MS/MS
trifluoroacetic acid [M þ H]þ
[M þ Na]þ
Viscosin group, Analytical Luna 5 mm C18, (A) 5 mmol/L ammonium acetate in Fraction A 6.5 ESI-MS [122]
cyclic LP 250 mm  4.60 mm water; (B) ACN, linear gradient from Fraction B 8.1/8.3 [M þ H]þ
a 25:75 ratio to a 0:100 ratio over a Fraction C 9.2 [M þ H]
time span of 15 min; flow rate of
1 mL/min.

miscible polar organic solvent, for example, ACN or generally require a relatively pure LP sample. The major-
methanol. Table 4 shows several LC-MS systems ity of LP analyzed by GC-MS requires chemical derivati-
designed for the analysis of LP. zation involving hydrolytic cleavage of the bond
LC-MS techniques are also highly efficient in separat- between the peptide and lipid portions of LP to provide
ing and purifying LP isoforms. Thus, an efficient high-re- volatility and thermal stability prior to analysis. The ana-
solution LC-MS method is a prerequisite for the lysis of LP involves hydrolytic cleavage of the bond
purification of microbial LP, which is required for subse- between the peptide part and lipid portions of LP.
quent commercialization of a particular LP isoforms as a Subsequent derivatization of resulting fatty acid chains
potential therapeutic agent.[123] LC-MS is best suited for to fatty acid methyl esters would facilitate GC or GC-MS
a discovery-based approach when working on unknown analysis.[124] GC-MS provides greater sensitivity than
LP, as many BS are readily amenable to LC-MS analysis. LC-MS for free fatty acids as the high resolution of GC
permits separation of structurally similar fatty acids that
would be very difficult to separate by HPLC. GC is not
Gas chromatography (GC)–MS
commonly used for the analysis of biomolecules since
GC is widely used in applications involving the structural samples (e.g. peptides) are thermally destroyed after
analysis of BS. Typical applications pertain to the quanti- hydrolysis. Smaller molecules, such as amino acids, fatty
tative and/or qualitative analysis of fatty acid structures. acids and certain carbohydrates, can be analyzed if they
When coupled to MS, it is possible to obtain additional are chemically modified to increase their volatility. While
information about the molecular mass of each sepa- GC is more sensitive, LC is more versatile as it is not
rated compound and its elemental composition, func- restricted to volatile and heat-stable samples; the LC
tional groups, and, in certain cases, molecular geometry sample only has to dissolve completely in the mobile
and spatial isomerism. The efficient GC-MS methods phase.
CRITICAL REVIEWS IN BIOTECHNOLOGY 403

GC-MS techniques have been used for resolving the may be divided into the following steps: (1) Establishing
structure of LP produced by B. thuringiensis.[125] GC-MS suitable conditions for recording spectra; (2) Measuring
was utilized in the identification of fatty acid moieties in a series of 1D (1H and 13C) or 2D (e.g. COZY, TOCSY and
purified LP where the LP was discovered to contain a ROSY) NMR spectra; (3) Integrating cross peaks and
C17 fatty acid with one double bond between carbons transformation into upper-distance bounds (calibration);
13 and 14.[125] In a study using GC-MS to analyze TLC- (4) Assessing the quality of the molecular structure.
purified LP, the GC analysis spectrum indicated that Samples are mixed with a reference compound solution
fatty acids portions of the LP contained 3-hydroxy tride- (e.g. tetramethylsilane dissolved in DMSO-d6 for 1H
canoate (3-OH-C13), tetradecanoate (3-OH-C14), pentade- NMR), added to an NMR probe (generally less than
canoate (3-OH-C15) and hexadecanoate (3-OH-C16).[126] 2 ml), inserted into the instrument, generating the NMR
A subsequent study identified GC-MS peaks that were spectrum for analysis.
characteristic of b-hydroxy fatty acid methyl deriva- NMR can be used to confirm LP structural identifica-
tives.[127] The purified active compound was hydro- tion of both the peptide and fatty acid portion while
lyzed with 6 M HCl at 110  C for 2 h in a sealed vial. Free simultaneously providing data on the position of link-
fatty acids were converted to methyl esters and ana- ages between the peptide and fatty acid chain. For LP
lyzed with a GC-MS. Peaks observed at m/z 74 and 103 NMR experiments, purified LP is dissolved in deuterated
(base peak) were characteristic for methyl derivatives of chloroform, and a series of 1D and 2D NMR experiments
b-hydroxy fatty acids. are carried out.[30] Results from NMR spectroscopy are
drawn from the NMR spectrum which depends on the
effect of shielding by electrons orbiting the nucleus.
Matrix-assisted laser desorption-ionization (MALDI)
Chemical shifts in the spectrum represent alterations or
time-of-flight (TOF) MS
changes in the molecular structure. The chemical shift
MALDI MS is a soft ionization MS technique that allows for 1H NMR (Figure 2A) is determined as the difference
the identification of intact compounds. In MALDI, an (in ppm) between the resonance frequency of the
analyte is first co-crystallized with a large molar excess observed proton and that of a reference proton present
of a matrix compound, typically a UV-absorbing weak in a reference compound set at 0 ppm. All 1D and 2D 1H
organic acid. The mixture is subsequently exposed to NMR spectra of LP produced by B. licheniformis were
laser radiation, resulting in the vaporization of the recorded at 299 K locked to the deuterium resonance of
matrix that carries the analyte with it. The matrix com- the solvent, DMSO-d6 (Figure 2B).[110] The NMR data
pound plays a key role by strongly absorbing the laser indicated that the peptide moiety contained seven
light energy, indirectly causing the analyte to vapor- amino acids per molecule. Complete amino acid spin
ize.[128] The matrix compound also serves as a proton systems and amino acid sequence were identified from
donor and acceptor and forces the analyte to ionize in a 2D 1H phase. NMR spectra indicated the presence of a
both the positive and negative ionization modes, long chain fatty acid, which contained a b-hydroxyl
respectively.[129] MALDI can be used to determine the group.
full molecular mass of purified LP/BS. Easy sample prep- The power of sophisticated techniques, such as
aration and recent developments in small bench top NMR spectroscopy for structural elucidation is
MALDI-TOF MS instruments have made this an attractive extremely appealing. It is tempting to believe that
technique for LP analysis. A recent report utilized structures determined by NMR application are
MALDI-TOF MS to identify surfactin LP.[17] In MS/MS unequivocal. A common mistake is to use a 13C NMR
sequencing, the lactone ring present in LP was cleaved carbon count to determine the molecular formula for a
by incubating each peptide with 10% NaOH in metha- LP. Although the elemental composition can be pre-
nol at room temperature for 16 h. The mass spectra of sumed by this procedure, it has not been conclusively
LP showed a series of mass number of m/z 1043 established.[131]
and assigned it to the LP group surfactin with m/z 637
and 985.
FT-IR
FT-IR spectroscopy is a rapid and inexpensive method to
NMR analysis of LP
characterize the chemical structure of BS and identify
NMR spectroscopy is an experimental method that can the functional groups present in LP. FT-IR is a physico-
provide structural information of molecules in solution chemical method based on measuring the vibrations of
with a high resolution. NMR spectroscopy is a high- a molecule excited by IR radiation at a specific wave-
throughput technique. Structure determination by NMR length range. This technique determines the functional
404 P. BINIARZ ET AL.

Figure 2. (A) 1H chemical shift positions of chemical groups in biomolecules [130] and (B) 2D 1H-1H TOCSY spectrum of a
Pseudomonas LP [122]

Figure 3. FTIR spectrum of a LP/BS produced by Candida tropicalis MTCC23 [133]

groups of gases, liquids, and solids and gives a structural As with any analytical techniques, FT-IR approaches
elucidation of a compound of interest. The presence or have certain advantages and disadvantages. FT-IR is
absence of functional groups, their protonation states, advantageous in that an IR spectrophotometer and the
or any changes due to new interactions can be moni- necessary software are readily available and can be
tored by analyzing the position and intensity of different used for routine analysis. In addition, FT-IR methods are
IR absorption bands. Despite some differences in FT-IR relatively fast, simple to use, and cheap and IR spectros-
spectra among LP or experimental conditions, the IR copy is nondestructive, i.e. the structure of LP remains
spectrophotometer is used in the range between unchanged during analysis. However, environmental
approximately 4000 and 400 cm1.[132] conditions around the FT-IR instrument can cause varia-
The interpretation of spectra and peak assignments tions in the spectra. Hence, background scans and
are key steps in the FT-IR analysis of LP. The wave num- repeated scans of the same sample are required. In add-
ber positions of absorbance peaks, peak intensities and ition, mixtures of BS may exhibit overlapping spectra,
peak widths are useful for functional group and sample leading to a misinterpretation of results; therefore, a
identification. There are several interesting peaks that proper purification step is required prior to performing
appear on an IR spectrum of a LP (Figure 3 and Table FT-IR.
S3), which are considered to be characteristic of FT-IR has been utilized in LP studies to identify the
LP.[134,135] type of LP. For example, FT-IR analysis of purified LP
CRITICAL REVIEWS IN BIOTECHNOLOGY 405

produced by B. circulans and standard surfactin identi- screening and initial steps of BS production, purification
fied the purified LP as surfactin.[136] The samples were and characterization is the ideal one.
dispersed in spectral grade KBr and measurements were In this review, we have presented a thorough investi-
carried out in the transmittance mode in the gation of various means of screening, production, isola-
400–4000 cm1 range. The FT-IR spectrum of the puri- tion, purification and structural characterization of LP.
fied compound showed transmittance at 1260 and Rapid advances in the last few years have helped us to
1900 cm1 that may be present due to the stretching understand the process of LP production by microor-
vibrations of C–O and C¼O. A single peak at 1590 cm1 ganisms. This knowledge will serve to increase the rate
corresponded to the deformation of N–H bonds, and a at which novel LP/BS can be identified and character-
strong NH bond was observed at 3420 cm1. FT-IR spec- ized to identify the molecules that have desirable char-
tra of the purified BS also has closely resembled the IR acteristics and would be useful in a multitude of fields.
absorption pattern displayed by other LP like surfac- There are still drawbacks in the available techniques for
tin,[90] fengycin,[19] iturin [106] and bacillomycin.[137]
rapid LP study, therefore, this area should be pursued.
The presence of lichenysin A in B. licheniformis BAS50
was confirmed using FT-IR.[110] Huang et al. [34] con-
ducted a quantitative analysis of LP using FT–IR spectra, Acknowledgements
which indicated the presence of the ester group. The authors would like to thank anonymous reviewers for
their comments and help with improving this manuscript.
This work was supported by Wroclaw Center of
Conclusions and perspectives
Biotechnology, program: The Leading National Research
Intensive development in biotechnology, genetic engin- Center (KNOW) for years 2014–2018.
eering and an increase in human responsibility for envir-
onmental protection contribute to the search for new Disclosure statement
microorganisms producing biomolecules that have
desirable characteristics and would be useful in a multi- The authors report no conflicts of interest. The authors alone
are responsible for the content and writing of the paper.
tude of fields. BS have the potential to be such an all-
purpose molecules in the future.
Over the years, BS and LP in particular have become
broadly pertinent in various industries and, therefore, References
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